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Conserved domains on  [gi|568931674|ref|XP_006539132|]
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msx2-interacting protein isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
 3484-3644 1.88e-97

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


:

Pssm-ID: 439206  Cd Length: 163  Bit Score: 311.45  E-value: 1.88e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3484 KYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGG---PPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALP 3560
Cdd:cd21543     1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNgnlPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3561 CGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNIsPHLMIV 3640
Cdd:cd21543    81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADI-PHLMIV 159


                  ....
gi 568931674 3641 IASV 3644
Cdd:cd21543   160 IATV 163
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 512-588 9.29e-47

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


:

Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 162.93  E-value: 9.29e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  512 FGKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 588
Cdd:cd12351     1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 438-511 3.90e-45

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


:

Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 158.34  E-value: 3.90e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 511
Cdd:cd12350     1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 338-411 5.23e-41

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


:

Pssm-ID: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 146.40  E-value: 5.23e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  338 GIKVQNLPVRSTDTSLKDGLFHEFKKFGKVTSVQIHGASEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12349     1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 7-81 2.81e-37

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


:

Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 135.82  E-value: 2.81e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKMGDRDLRTDYNEP 81
Cdd:cd12348     1 HLWVGNLPENVREEKIIEHFKRFGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHSAVNKMGGRDLRTDYNEP 75
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 1629-2063 1.08e-10

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 68.43  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1629 PETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAgekPAEPAPVSEETKLVSEPASV 1708
Cdd:PHA03247 2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP---PPSPSPAANEPDPHPPPTVP 2647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1709 PVEQPRQSDVPPgedsRDSQDSAALAPSAPQESAATDAVPCVNAEPltpgTTVSQVESSVDPKP------SSPQPLSKLT 1782
Cdd:PHA03247 2648 PPERPRDDPAPG----RVSRPRRARRLGRAAQASSPPQRPRRRAAR----PTVGSLTSLADPPPppptpePAPHALVSAT 2719

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1783 QRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA-QPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVtr 1861
Cdd:PHA03247 2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGpARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES-- 2797

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1862 kseridreklkrSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTehPEPSLPLSRSRRRNVRSVYATMT-------DHE 1934
Cdd:PHA03247 2798 ------------LPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPPPPSLPLGgsvapggDVR 2863

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1935 SRSPAKEPVEQP---------RVTRKRLERELQEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSPRS 2005
Cdd:PHA03247 2864 RRPPSRSPAAKPaaparppvrRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674 2006 QKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPST 2063
Cdd:PHA03247 2944 APTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
PTZ00121 super family cl31754
MAEBL; Provisional
 635-1272 7.98e-10

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.55  E-value: 7.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  635 AQSPHKCREERRgsyeySQERTYYENVRTPgtypEDSRRDYPARGREFYSEWETYQGEYYDSRYYDEPREYREYRSDPyE 714
Cdd:PTZ00121 1190 AEELRKAEDARK-----AEAARKAEEERKA----EEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFE-E 1259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  715 QDIREYSYRQRERERERERFESD--------------RDHERRPIERSQSPVHLRRPQSPGVSPAHSERLPSDSERRLYR 780
Cdd:PTZ00121 1260 ARMAHFARRQAAIKAEEARKADElkkaeekkkadeakKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAE 1339

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  781 RSSERSGSCSSVSPPRYDKLEKARlerytKNEKADKERTfdpERVERERRIVRKEKGEKDKAERQKRKGKAHSPSSQPSE 860
Cdd:PTZ00121 1340 EAKKAAEAAKAEAEAAADEAEAAE-----EKAEAAEKKK---EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELK 1411

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  861 TEQENDREQSPEKPRGSTKLSRDRADKEGPAKNRLELVpcvvltRVKEKEGKVIEHPPP---EKLKA-RLGRDTTKASAL 936
Cdd:PTZ00121 1412 KAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEA------KKKAEEAKKAEEAKKkaeEAKKAdEAKKKAEEAKKA 1485

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  937 DQKPQAAQGEPAKSDPARGKALREKVLPSHAEVGEKEGRTKLRKHLKAEQTPELSALDlEKLEARKRRFADSGLKIE-KQ 1015
Cdd:PTZ00121 1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAE-EKKKADELKKAEELKKAEeKK 1564

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1016 KPEIKKTSPETEDT---RILLKKQPDTSRDGVLLREGESERKPVRKEILKRESKKTKLERLNSALSPKDCQDPAAVSAGS 1092
Cdd:PTZ00121 1565 KAEEAKKAEEDKNMalrKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAE 1644

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1093 GSRPSSDVHAglgelthgsvETQETQPKKAIPSKPQPKQLQLLENQGPEKEEVRKNYCRPREEPAEHRAGQEKPHGGNAE 1172
Cdd:PTZ00121 1645 EKKKAEELKK----------AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEE 1714

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1173 EKLGIDIDHTQSYRK-QMEQSRRKQrmEMEIAKAEKFgspkkDVDDYERRSLVHEVGKPPQDVTDDSPPSKKRRTDHVDF 1251
Cdd:PTZ00121 1715 KKKAEELKKAEEENKiKAEEAKKEA--EEDKKKAEEA-----KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDE 1787

                         650       660
                  ....*....|....*....|.
gi 568931674 1252 DICTKRERNYRSSRQISEDSE 1272
Cdd:PTZ00121 1788 EDEKRRMEVDKKIKDIFDNFA 1808
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2949-3474 5.87e-08

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.57  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2949 PANLGPTLTPHHPPALP------------SKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPRPTGPT-------PGL 3009
Cdd:PHA03247 2512 PSRLAPAILPDEPVGEPvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAvtsrarrPDA 2591

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3010 FPRPCHPSSTTSTALSTNATVMLAAGIPVPqfissiHPEQSVIMPPHSITQTVSLGHLSQGEVRMSTPTLPSITYSIRPE 3089
Cdd:PHA03247 2592 PPQSARPRAPVDDRGDPRGPAPPSPLPPDT------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3090 TLHSPRAPLQPQQiEARAPQRVGTPqPATTGVPALATQHPPEEEVHyhlPVARAAAPVQSEVLVMQSEYRLHPYT----- 3164
Cdd:PHA03247 2666 RARRLGRAAQASS-PPQRPRRRAAR-PTVGSLTSLADPPPPPPTPE---PAPHALVSATPLPPGPAAARQASPALpaapa 2740

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3165 ---------VPRDVRIMVHPHVTAVSEQPRATEGVVKVPPANKAPQQLVKEAVKTSDAKAVPAPAPVPVPVPVPTPAPPP 3235
Cdd:PHA03247 2741 ppavpagpaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3236 HGEARILTVTPSSQLQGLPLTPPVVVTHGVQIVHSSGELFQEYRYGDVRTyhAPAQQLTHTQFPVASSISLA-SRTKTSA 3314
Cdd:PHA03247 2821 AASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS--PAAKPAAPARPPVRRLARPAvSRSTESF 2898

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3315 QVPPEGEPLQSTQSAQPAPSTQATqpiPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEP 3394
Cdd:PHA03247 2899 ALPPDQPERPPQPQAPPPPQPQPQ---PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3395 HAQL--QRAPVETAQPAHPSPVSVSMkPDLPSPLSSQA----------APKQPLFVPANSGPSTPPGLALPHAE------ 3456
Cdd:PHA03247 2976 RFRVpqPAPSREAPASSTPPLTGHSL-SRVSSWASSLAlheetdpppvSLKQTLWPPDDTEDSDADSLFDSDSErsdlea 3054

                         570
                  ....*....|....*...
gi 568931674 3457 VQPAPKQESSPHGTPQRP 3474
Cdd:PHA03247 3055 LDPLPPEPHDPFAHEPDP 3072
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 2122-2642 3.40e-05

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 3.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2122 EAGPAAASPqeSESPQKGSGSSPQLANNPADPDREAEEESASASTAPPEGTQLARQIElEQAVQNIAKLPEPSAAAASKG 2201
Cdd:PHA03247 2486 ARFPFAAGA--APDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLE-ELASDDAGDPPPPLPPAAPPA 2562

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2202 TATATAASEEPAPEHGhKPAHQASETELAA----AIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGLHEAESGIL 2277
Cdd:PHA03247 2563 APDRSVPPPRPAPRPS-EPAVTSRARRPDAppqsARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPH 2641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2278 ETGTATESSAPQVSAL--------------DPPEGSADTKETR--------GNSGDSVQ-EAKGSKVEVTPPRKDKGRQK 2334
Cdd:PHA03247 2642 PPPTVPPPERPRDDPApgrvsrprrarrlgRAAQASSPPQRPRrraarptvGSLTSLADpPPPPPTPEPAPHALVSATPL 2721

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2335 TTRRRKRNANKKVVAITETRASEAEQTQSESPAAEEATAATPEAPQEEKQSEKPPSPPAECTFDPSKTPPAESLSQENSA 2414
Cdd:PHA03247 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2415 AEKTPCKAPVL---PALPPLSQPALMDDGPQArfkvhsiieSDPVTPPSDSGIPPPTIPLVTiAKLPPPVIPGGVPHQSP 2491
Cdd:PHA03247 2802 WDPADPPAAVLapaAALPPAASPAGPLPPPTS---------AQPTAPPPPPGPPPPSLPLGG-SVAPGGDVRRRPPSRSP 2871

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2492 PPKVTEwitrQEEPRAQSTPSPALPPDTKAsdmdtssstlrkiLMDPKYVSATGVTSTSVTSAIAEPVSAPCLQEAPAPP 2571
Cdd:PHA03247 2872 AAKPAA----PARPPVRRLARPAVSRSTES-------------FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674 2572 CDPKHPPlegvsaAAVPNADTQASEVPVAADKEKVAPVIAPkitsviSRMPVSIDLENSQKITLAKPAPQT 2642
Cdd:PHA03247 2935 PPPRPQP------PLAPTTDPAGAGEPSGAVPQPWLGALVP------GRVAVPRFRVPQPAPSREAPASST 2993
Collagen_mid super family cl24528
Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial ...
 2641-2719 6.49e-04

Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.


The actual alignment was detected with superfamily member pfam15984:

Pssm-ID: 435053 [Multi-domain]  Cd Length: 198  Bit Score: 43.86  E-value: 6.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  2641 QTLTGLVSALTGLVNVSLVPVNALKGPVKGSVATLKGLVSTPAGPVN--LLKGPVNVLTGPVNVLTTPVSATVG----TV 2714
Cdd:pfam15984   60 NAVTSAGQLVSGLGTGPLAPLAPVTTPLGGTVSTLGGAVTGGGTTLGtaLSTGPVQQLTQQVSSAITPITSTVTgttqTV 139


                   ....*
gi 568931674  2715 NAAPG 2719
Cdd:pfam15984  140 GAATG 144
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 128-596 6.89e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.19  E-value: 6.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   128 RYERRLdgasdnRERAYEHSAYGHHERgtgafDRTRHYDQDYYRDPRERTLQHGLYYTSRSRSPNRFDAhdprYEPRARE 207
Cdd:TIGR01642    3 EEPDRE------REKSRGRDRDRSSER-----PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS----RSPRSLR 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   208 QFTLPSVVHRDIYRD-DITREVRGRRPERSyqhsrsrsphssqsrnQSPQRLASQASRPTRSPSGSGSRSRSSSSDSISS 286
Cdd:TIGR01642   68 YSSVRRSRDRPRRRSrSVRSIEQHRRRLRD----------------RSPSNQWRKDDKKRSLWDIKPPGYELVTADQAKA 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   287 SSSSSSNTDSSDSSSTASDDSPARSVQSAAVPAPtsqllsSLEKDEPRKSFGIKVQNLPVRSTDTSLKDGLFHEFKKFGK 366
Cdd:TIGR01642  132 SQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVL------PYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGY 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   367 --------VTSVQIHgaSEERYGLVFFRQQEDQEKALtASKGKLFFGMQIEV----------TAWVGPETESENEFRPLD 428
Cdd:TIGR01642  206 hkaedgkhVSSVNIN--KEKNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIrrphdyipvpQITPEVSQKNPDDNAKNV 282

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   429 ERIDEFH--PKATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIKKMDGEYL 503
Cdd:TIGR01642  283 EKLVNSTtvLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKdiATGLSKgYAFCEYKDPSVTDVAIAALNGKDT 362

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   504 GNNRL---KLGFGKSMPT-------------------NCVWLDGLSSNV--------------SDQY------LTRHFCR 541
Cdd:TIGR01642  363 GDNKLhvqRACVGANQATidtsngmapvtllakalsqSILQIGGKPTKVvqltnlvtgddlmdDEEYeeiyedVKTEFSK 442

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674   542 YGPVVKVVFDRLK---------GMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQLA 596
Cdd:TIGR01642  443 YGPLINIVIPRPNgdrnstpgvGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCYKA 506
 
Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
 3484-3644 1.88e-97

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439206  Cd Length: 163  Bit Score: 311.45  E-value: 1.88e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3484 KYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGG---PPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALP 3560
Cdd:cd21543     1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNgnlPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3561 CGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNIsPHLMIV 3640
Cdd:cd21543    81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADI-PHLMIV 159


                  ....
gi 568931674 3641 IASV 3644
Cdd:cd21543   160 IATV 163
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 512-588 9.29e-47

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 162.93  E-value: 9.29e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  512 FGKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 588
Cdd:cd12351     1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 438-511 3.90e-45

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 158.34  E-value: 3.90e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 511
Cdd:cd12350     1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 338-411 5.23e-41

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 146.40  E-value: 5.23e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  338 GIKVQNLPVRSTDTSLKDGLFHEFKKFGKVTSVQIHGASEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12349     1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 7-81 2.81e-37

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 135.82  E-value: 2.81e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKMGDRDLRTDYNEP 81
Cdd:cd12348     1 HLWVGNLPENVREEKIIEHFKRFGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHSAVNKMGGRDLRTDYNEP 75
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
 3481-3644 2.37e-28

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 112.83  E-value: 2.37e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3481 LKQKYPIVWQGLLALKN-DTAAVQLHFVSGNNVLAHRSLplseggppLRIAQRMRLEASQ--LEGVARRMTveTDYCLLL 3557
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL--------LRITGRIRLDAVWkyLDEVRRSIT--RDVLVVR 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3558 ALPCgrDQEDVVSQTEslkaaFITYLQAKQAAGIInvpNPGSNQpAYVLQIFPPCEFSESHLSRlapDLLASISNiSPHL 3637
Cdd:pfam07744   71 FFPS--SESDESAFDE-----LIDYLQSKQRAGVI---HAKSAD-VKDLYLFPPCEFLELLLPV---GLSLEVSE-PNLL 135


                   ....*..
gi 568931674  3638 MIVIASV 3644
Cdd:pfam07744  136 LGVVVRK 142
RRM smart00360
RNA recognition motif;
441-510 7.97e-15

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.86  E-value: 7.97e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLvrDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 339-594 9.06e-15

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 80.62  E-value: 9.06e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   339 IKVQNLPvRSTDTSlkdGLFHEFKKFGKVTSVQIhgASEER-----YGLVFFRQQEDQEKALTASKGKLFFGMQIevtaW 413
Cdd:TIGR01628   91 IFVKNLD-KSVDNK---ALFDTFSKFGNILSCKV--ATDENgksrgYGFVHFEKEESAKAAIQKVNGMLLNDKEV----Y 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   414 VGPeteseneFRPLDERIDEFHPKATrTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQYAFLQYCDIASV 491
Cdd:TIGR01628  161 VGR-------FIKKHEREAAPLKKFT-NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKdgSGRSRGFAFVNFEKHEDA 232

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   492 CKAIKKMDGEYLGN----NRLKLG-----------------------FGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGP 544
Cdd:TIGR01628  233 AKAVEEMNGKKIGLakegKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGE 311

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 568931674   545 VV--KVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQ 594
Cdd:TIGR01628  312 ITsaKVMLDekgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ 366
RRM smart00360
RNA recognition motif;
8-75 9.41e-13

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 65.69  E-value: 9.41e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674      8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGfAFVEFESEEDAEKALEALNgkELDGRPLK 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 442-509 4.69e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 63.79  E-value: 4.69e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLvRDETGRSKgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
520-586 1.39e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 62.61  E-value: 1.39e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    520 CVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVesVRLVRDketgKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 8-75 6.24e-11

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 60.71  E-value: 6.24e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674     8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNgkELGGRELK 70
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1629-2063 1.08e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 68.43  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1629 PETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAgekPAEPAPVSEETKLVSEPASV 1708
Cdd:PHA03247 2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP---PPSPSPAANEPDPHPPPTVP 2647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1709 PVEQPRQSDVPPgedsRDSQDSAALAPSAPQESAATDAVPCVNAEPltpgTTVSQVESSVDPKP------SSPQPLSKLT 1782
Cdd:PHA03247 2648 PPERPRDDPAPG----RVSRPRRARRLGRAAQASSPPQRPRRRAAR----PTVGSLTSLADPPPppptpePAPHALVSAT 2719

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1783 QRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA-QPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVtr 1861
Cdd:PHA03247 2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGpARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES-- 2797

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1862 kseridreklkrSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTehPEPSLPLSRSRRRNVRSVYATMT-------DHE 1934
Cdd:PHA03247 2798 ------------LPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPPPPSLPLGgsvapggDVR 2863

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1935 SRSPAKEPVEQP---------RVTRKRLERELQEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSPRS 2005
Cdd:PHA03247 2864 RRPPSRSPAAKPaaparppvrRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674 2006 QKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPST 2063
Cdd:PHA03247 2944 APTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
PTZ00121 PTZ00121
MAEBL; Provisional
 635-1272 7.98e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.55  E-value: 7.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  635 AQSPHKCREERRgsyeySQERTYYENVRTPgtypEDSRRDYPARGREFYSEWETYQGEYYDSRYYDEPREYREYRSDPyE 714
Cdd:PTZ00121 1190 AEELRKAEDARK-----AEAARKAEEERKA----EEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFE-E 1259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  715 QDIREYSYRQRERERERERFESD--------------RDHERRPIERSQSPVHLRRPQSPGVSPAHSERLPSDSERRLYR 780
Cdd:PTZ00121 1260 ARMAHFARRQAAIKAEEARKADElkkaeekkkadeakKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAE 1339

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  781 RSSERSGSCSSVSPPRYDKLEKARlerytKNEKADKERTfdpERVERERRIVRKEKGEKDKAERQKRKGKAHSPSSQPSE 860
Cdd:PTZ00121 1340 EAKKAAEAAKAEAEAAADEAEAAE-----EKAEAAEKKK---EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELK 1411

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  861 TEQENDREQSPEKPRGSTKLSRDRADKEGPAKNRLELVpcvvltRVKEKEGKVIEHPPP---EKLKA-RLGRDTTKASAL 936
Cdd:PTZ00121 1412 KAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEA------KKKAEEAKKAEEAKKkaeEAKKAdEAKKKAEEAKKA 1485

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  937 DQKPQAAQGEPAKSDPARGKALREKVLPSHAEVGEKEGRTKLRKHLKAEQTPELSALDlEKLEARKRRFADSGLKIE-KQ 1015
Cdd:PTZ00121 1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAE-EKKKADELKKAEELKKAEeKK 1564

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1016 KPEIKKTSPETEDT---RILLKKQPDTSRDGVLLREGESERKPVRKEILKRESKKTKLERLNSALSPKDCQDPAAVSAGS 1092
Cdd:PTZ00121 1565 KAEEAKKAEEDKNMalrKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAE 1644

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1093 GSRPSSDVHAglgelthgsvETQETQPKKAIPSKPQPKQLQLLENQGPEKEEVRKNYCRPREEPAEHRAGQEKPHGGNAE 1172
Cdd:PTZ00121 1645 EKKKAEELKK----------AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEE 1714

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1173 EKLGIDIDHTQSYRK-QMEQSRRKQrmEMEIAKAEKFgspkkDVDDYERRSLVHEVGKPPQDVTDDSPPSKKRRTDHVDF 1251
Cdd:PTZ00121 1715 KKKAEELKKAEEENKiKAEEAKKEA--EEDKKKAEEA-----KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDE 1787

                         650       660
                  ....*....|....*....|.
gi 568931674 1252 DICTKRERNYRSSRQISEDSE 1272
Cdd:PTZ00121 1788 EDEKRRMEVDKKIKDIFDNFA 1808
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2949-3474 5.87e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.57  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2949 PANLGPTLTPHHPPALP------------SKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPRPTGPT-------PGL 3009
Cdd:PHA03247 2512 PSRLAPAILPDEPVGEPvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAvtsrarrPDA 2591

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3010 FPRPCHPSSTTSTALSTNATVMLAAGIPVPqfissiHPEQSVIMPPHSITQTVSLGHLSQGEVRMSTPTLPSITYSIRPE 3089
Cdd:PHA03247 2592 PPQSARPRAPVDDRGDPRGPAPPSPLPPDT------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3090 TLHSPRAPLQPQQiEARAPQRVGTPqPATTGVPALATQHPPEEEVHyhlPVARAAAPVQSEVLVMQSEYRLHPYT----- 3164
Cdd:PHA03247 2666 RARRLGRAAQASS-PPQRPRRRAAR-PTVGSLTSLADPPPPPPTPE---PAPHALVSATPLPPGPAAARQASPALpaapa 2740

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3165 ---------VPRDVRIMVHPHVTAVSEQPRATEGVVKVPPANKAPQQLVKEAVKTSDAKAVPAPAPVPVPVPVPTPAPPP 3235
Cdd:PHA03247 2741 ppavpagpaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3236 HGEARILTVTPSSQLQGLPLTPPVVVTHGVQIVHSSGELFQEYRYGDVRTyhAPAQQLTHTQFPVASSISLA-SRTKTSA 3314
Cdd:PHA03247 2821 AASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS--PAAKPAAPARPPVRRLARPAvSRSTESF 2898

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3315 QVPPEGEPLQSTQSAQPAPSTQATqpiPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEP 3394
Cdd:PHA03247 2899 ALPPDQPERPPQPQAPPPPQPQPQ---PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3395 HAQL--QRAPVETAQPAHPSPVSVSMkPDLPSPLSSQA----------APKQPLFVPANSGPSTPPGLALPHAE------ 3456
Cdd:PHA03247 2976 RFRVpqPAPSREAPASSTPPLTGHSL-SRVSSWASSLAlheetdpppvSLKQTLWPPDDTEDSDADSLFDSDSErsdlea 3054

                         570
                  ....*....|....*...
gi 568931674 3457 VQPAPKQESSPHGTPQRP 3474
Cdd:PHA03247 3055 LDPLPPEPHDPFAHEPDP 3072
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
8-75 3.97e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 50.10  E-value: 3.97e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRgsEGGVA---AFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:COG0724     4 IYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDR--ETGRSrgfGFVEMPDDEEAQAAIEALNgaELMGRTLK 74
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 521-585 4.85e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 4.85e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   521 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIK 585
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIksIRLVRDetgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
339-410 6.64e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.13  E-value: 6.64e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    339 IKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQI-----HGASeERYGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:smart00360    2 LFVGNLPPDTTEEELRE----LFSKFGKVESVRLvrdkeTGKS-KGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
 432-571 1.18e-05

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 50.79  E-value: 1.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   432 DEFHPKATRTLFIGN-LEKTTTYHDLRNIFQRFGEIVDIDIK---KVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNR 507
Cdd:TIGR01659   99 DDNDTNNSGTNLIVNyLPQDMTDRELYALFRTIGPINTCRIMrdyKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674   508 LKLGF----GKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVK--VVFDRL----KGMALVLYSEIEDAQAAV 571
Cdd:TIGR01659  179 LKVSYarpgGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQknILRDKLtgtpRGVAFVRFNKREEAQEAI 252
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
439-509 1.24e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.86  E-value: 1.24e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLItdRETGRSRgFGFVEMPDDEEAQAAIEALNGAELMGRTLK 74
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2122-2642 3.40e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 3.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2122 EAGPAAASPqeSESPQKGSGSSPQLANNPADPDREAEEESASASTAPPEGTQLARQIElEQAVQNIAKLPEPSAAAASKG 2201
Cdd:PHA03247 2486 ARFPFAAGA--APDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLE-ELASDDAGDPPPPLPPAAPPA 2562

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2202 TATATAASEEPAPEHGhKPAHQASETELAA----AIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGLHEAESGIL 2277
Cdd:PHA03247 2563 APDRSVPPPRPAPRPS-EPAVTSRARRPDAppqsARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPH 2641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2278 ETGTATESSAPQVSAL--------------DPPEGSADTKETR--------GNSGDSVQ-EAKGSKVEVTPPRKDKGRQK 2334
Cdd:PHA03247 2642 PPPTVPPPERPRDDPApgrvsrprrarrlgRAAQASSPPQRPRrraarptvGSLTSLADpPPPPPTPEPAPHALVSATPL 2721

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2335 TTRRRKRNANKKVVAITETRASEAEQTQSESPAAEEATAATPEAPQEEKQSEKPPSPPAECTFDPSKTPPAESLSQENSA 2414
Cdd:PHA03247 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2415 AEKTPCKAPVL---PALPPLSQPALMDDGPQArfkvhsiieSDPVTPPSDSGIPPPTIPLVTiAKLPPPVIPGGVPHQSP 2491
Cdd:PHA03247 2802 WDPADPPAAVLapaAALPPAASPAGPLPPPTS---------AQPTAPPPPPGPPPPSLPLGG-SVAPGGDVRRRPPSRSP 2871

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2492 PPKVTEwitrQEEPRAQSTPSPALPPDTKAsdmdtssstlrkiLMDPKYVSATGVTSTSVTSAIAEPVSAPCLQEAPAPP 2571
Cdd:PHA03247 2872 AAKPAA----PARPPVRRLARPAVSRSTES-------------FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674 2572 CDPKHPPlegvsaAAVPNADTQASEVPVAADKEKVAPVIAPkitsviSRMPVSIDLENSQKITLAKPAPQT 2642
Cdd:PHA03247 2935 PPPRPQP------PLAPTTDPAGAGEPSGAVPQPWLGALVP------GRVAVPRFRVPQPAPSREAPASST 2993
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
 510-593 8.51e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 45.41  E-value: 8.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  510 LGFGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNK 583
Cdd:PLN03134   27 LGSLRLMSTK-LFIGGLSWGTDDASLRDAFAHFGDVVdaKVIVDRetgrSRGFGFVNFNDEGAATAAISEMDGKELNGRH 105

                          90
                  ....*....|
gi 568931674  584 IKVDFANRES 593
Cdd:PLN03134  106 IRVNPANDRP 115
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 339-409 1.52e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 42.61  E-value: 1.52e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674   339 IKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQI----HGASeERYGLVFFRQQEDQEKALTASKGKLFFGMQIE 409
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKD----LFSKFGPIKSIRLvrdeTGRS-KGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
Collagen_mid pfam15984
Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial ...
 2641-2719 6.49e-04

Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.


Pssm-ID: 435053 [Multi-domain]  Cd Length: 198  Bit Score: 43.86  E-value: 6.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  2641 QTLTGLVSALTGLVNVSLVPVNALKGPVKGSVATLKGLVSTPAGPVN--LLKGPVNVLTGPVNVLTTPVSATVG----TV 2714
Cdd:pfam15984   60 NAVTSAGQLVSGLGTGPLAPLAPVTTPLGGTVSTLGGAVTGGGTTLGtaLSTGPVQQLTQQVSSAITPITSTVTgttqTV 139


                   ....*
gi 568931674  2715 NAAPG 2719
Cdd:pfam15984  140 GAATG 144
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 3288-3480 6.62e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.80  E-value: 6.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3288 APAQQLTHTQFPVASSISLASRTKTSAQvppEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAQPPSGKIPQVS 3367
Cdd:pfam09770  170 AAAPAPAPQPAAQPASLPAPSRKMMSLE---EVEAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQP 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3368 QEAKGtqtggveqtrlPAIPTNRPSEPHAQLQRAPVETAQPAHPSPVSVSmKPDLPSPLSSQAAPKQPL-----FVPANS 3442
Cdd:pfam09770  247 QQQPQ-----------QPQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQA-QQFHQQPPPVPVQPTQILqnpnrLSAARV 314

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 568931674  3443 GPSTPPGLALPHAEVQPAPKQESSPHGTPQ---RPVDMVQL 3480
Cdd:pfam09770  315 GYPQNPQPGVQPAPAHQAHRQQGSFGRQAPiitHPQQLAQL 355
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
 442-518 2.43e-03

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 41.18  E-value: 2.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKSMPT 518
Cdd:PLN03134   37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVivdRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 128-596 6.89e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.19  E-value: 6.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   128 RYERRLdgasdnRERAYEHSAYGHHERgtgafDRTRHYDQDYYRDPRERTLQHGLYYTSRSRSPNRFDAhdprYEPRARE 207
Cdd:TIGR01642    3 EEPDRE------REKSRGRDRDRSSER-----PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS----RSPRSLR 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   208 QFTLPSVVHRDIYRD-DITREVRGRRPERSyqhsrsrsphssqsrnQSPQRLASQASRPTRSPSGSGSRSRSSSSDSISS 286
Cdd:TIGR01642   68 YSSVRRSRDRPRRRSrSVRSIEQHRRRLRD----------------RSPSNQWRKDDKKRSLWDIKPPGYELVTADQAKA 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   287 SSSSSSNTDSSDSSSTASDDSPARSVQSAAVPAPtsqllsSLEKDEPRKSFGIKVQNLPVRSTDTSLKDGLFHEFKKFGK 366
Cdd:TIGR01642  132 SQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVL------PYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGY 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   367 --------VTSVQIHgaSEERYGLVFFRQQEDQEKALtASKGKLFFGMQIEV----------TAWVGPETESENEFRPLD 428
Cdd:TIGR01642  206 hkaedgkhVSSVNIN--KEKNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIrrphdyipvpQITPEVSQKNPDDNAKNV 282

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   429 ERIDEFH--PKATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIKKMDGEYL 503
Cdd:TIGR01642  283 EKLVNSTtvLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKdiATGLSKgYAFCEYKDPSVTDVAIAALNGKDT 362

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   504 GNNRL---KLGFGKSMPT-------------------NCVWLDGLSSNV--------------SDQY------LTRHFCR 541
Cdd:TIGR01642  363 GDNKLhvqRACVGANQATidtsngmapvtllakalsqSILQIGGKPTKVvqltnlvtgddlmdDEEYeeiyedVKTEFSK 442

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674   542 YGPVVKVVFDRLK---------GMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQLA 596
Cdd:TIGR01642  443 YGPLINIVIPRPNgdrnstpgvGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCYKA 506
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1936-2203 8.46e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.17  E-value: 8.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1936 RSPAKEPVEQPRVTRKRlerelQEAVVPPTTPRRGRPPKTRRRAEedgeherkePAETPRPAEGWRSPRSQKSAAAAGPQ 2015
Cdd:PRK12323  375 ATAAAAPVAQPAPAAAA-----PAAAAPAPAAPPAAPAAAPAAAA---------AARAVAAAPARRSPAPEALAAARQAS 440

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2016 GKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPveVLERKPPEKtykskrgrARST 2095
Cdd:PRK12323  441 ARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP--PWEELPPEF--------ASPA 510

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2096 RSAMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLANNPADPDREAEEESASAS------TAPP 2169
Cdd:PRK12323  511 PAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMFDGDwpalaaRLPV 590

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 568931674 2170 EG--TQLARQIELEQAVQNIAKLPEPSAAAASKGTA 2203
Cdd:PRK12323  591 RGlaQQLARQSELAGVEGDTVRLRVPVPALAEAEVV 626
 
Name Accession Description Interval E-value
SPOC_SHARP cd21543
SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor ...
 3484-3644 1.88e-97

SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439206  Cd Length: 163  Bit Score: 311.45  E-value: 1.88e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3484 KYPIVWQGLLALKNDTAAVQLHFVSGNNVLAHRSLPLSEGG---PPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALP 3560
Cdd:cd21543     1 RYPVVWQGLLALKNDEAAVQMHYVSGNQDLAKRSLPRHLTNgnlPPLRIAQRMRLEPSQLEGVARKMQDESEYCLLLALP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3561 CGRDQEDVVSQTESLKAAFITYLQAKQAAGIINVPNPGSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNIsPHLMIV 3640
Cdd:cd21543    81 CGRDQEDVLKQTNNLKNGFITYLQQKQAAGIVNVPNPGSQQPAYVVHIFPPCEFSNSHLSRLAPDLLNSIADI-PHLMIV 159


                  ....
gi 568931674 3641 IASV 3644
Cdd:cd21543   160 IATV 163
SPOC_SF cd21520
SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in ...
 3488-3642 1.39e-52

SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in developmental signalling and has also been proposed to be a phosphorylation binding module. It has been found mainly in two protein families: transcription factor S-II (TFIIS) and Spen (split end). The TFIIS family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. The Spen protein family includes SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). They are characterized by containing RNA recognition motifs (RRMs) and a SPOC domain.


Pssm-ID: 439200  Cd Length: 138  Bit Score: 182.10  E-value: 1.39e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3488 VWQGLLALKND-TAAVQLHFVSGNNVLAhrslpLSEGGPPLRIAQRMRLEASQLEGVARRMTVETDYCLLLALPCGRDQe 3566
Cdd:cd21520     1 VWQGLLALKNDpTAAARLHFVSGNNVLA-----LSELPPVLRIAQRMRLNATQLEGVARRMAVATDYCLVLALPCGRDD- 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674 3567 dvvsqtESLKAAFITYLQAKQAAGIInvpnpgSNQPAYVLQIFPPCEFSESHLSRLAPDLLASISNISPHLMIVIA 3642
Cdd:cd21520    75 ------ESLKAAFITYLQAKQRAGIA------SNQPAYVLQLFPPCEFSESHLSRLAPDLLASIVTISPHLMIVIL 138
SPOC_Spen cd21539
SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein ...
 3488-3642 1.43e-49

SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein family; The Spen protein family includes a group of proteins characterized by containing RNA recognition motifs (RRMs) and a SPOC domain, such as SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs), and components of the NuRD complex. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. Chp1p is a component of the kinetochore which plays a role in stabilizing microtubules and thus, allowing accurate chromosome segregation. It has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439202  Cd Length: 148  Bit Score: 173.84  E-value: 1.43e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3488 VWQGLLALKNDTAAVQLHFVSGNNVLAH-RSLPLSEGGPPLRIAQRMRLEASQLEGvaRRMTVETDYCLLLALPCGRDQE 3566
Cdd:cd21539     1 IWRGVLLVKNSAFLFRCHLAKGDAEIASqQLLRETVSCPQVDIVQRMRLDELALFE--RSGAVATGLAILLALPCGDDSI 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674 3567 DVVSQTESLKAAFITYLQAKQAAGIINVPNPgsnQPAYVLQIFPPCEFSESHLSRLapdLLASISNISPHLMIVIA 3642
Cdd:cd21539    79 SSASITEAPLTNFVSYLKAKQAAGVVLLSDD---HENYVLLLFPPSEFSLSLLKRS---LNSEQATSDSYLVMVVV 148
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 512-588 9.29e-47

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 162.93  E-value: 9.29e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  512 FGKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 588
Cdd:cd12351     1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 438-511 3.90e-45

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 158.34  E-value: 3.90e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 511
Cdd:cd12350     1 ATRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 338-411 5.23e-41

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 146.40  E-value: 5.23e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  338 GIKVQNLPVRSTDTSLKDGLFHEFKKFGKVTSVQIHGASEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12349     1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 7-81 2.81e-37

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 135.82  E-value: 2.81e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKMGDRDLRTDYNEP 81
Cdd:cd12348     1 HLWVGNLPENVREEKIIEHFKRFGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHSAVNKMGGRDLRTDYNEP 75
SPOC_RBM15-like cd21544
SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 ...
 3488-3641 4.42e-32

SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 (RBM15) and similar proteins; This subfamily includes RBM15, RBM15B, and similar proteins found in metazoans. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as a receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. Members of this family have a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439207  Cd Length: 164  Bit Score: 124.31  E-value: 4.42e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3488 VWQGLLALKNDTAAVQLHFVSGNNVLA--HRSLPLSEGGPPLRIAQRMRLEASQLEGVARRMTVETD--YCLLLALP--C 3561
Cdd:cd21544     1 VWSGALVLKNSAFPVRMHLLRGDVQLAdtLLPNPTSGEQPVLRITQRLRLDPPKLDDVSRRISSAGSsgYCVLLAVPgsG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3562 GRDQEDVVSQTESLKaAFITYLQAKQAAGIINVPNPGSNQP---AYVLQIFPPCEFSESHLSRLAPDLLASISNISpHLM 3638
Cdd:cd21544    81 ANSEADASTQQRPLR-NLVSYLKQKEAAGVVSLPPNGSVGEkkvTGVLHAFPPCDFSQQLLRRLAPSLSLESLKDD-HLV 158


                  ...
gi 568931674 3639 IVI 3641
Cdd:cd21544   159 IVL 161
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
 3481-3644 2.37e-28

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 112.83  E-value: 2.37e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3481 LKQKYPIVWQGLLALKN-DTAAVQLHFVSGNNVLAHRSLplseggppLRIAQRMRLEASQ--LEGVARRMTveTDYCLLL 3557
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL--------LRITGRIRLDAVWkyLDEVRRSIT--RDVLVVR 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3558 ALPCgrDQEDVVSQTEslkaaFITYLQAKQAAGIInvpNPGSNQpAYVLQIFPPCEFSESHLSRlapDLLASISNiSPHL 3637
Cdd:pfam07744   71 FFPS--SESDESAFDE-----LIDYLQSKQRAGVI---HAKSAD-VKDLYLFPPCEFLELLLPV---GLSLEVSE-PNLL 135


                   ....*..
gi 568931674  3638 MIVIASV 3644
Cdd:pfam07744  136 LGVVVRK 142
SPOC_RBM15 cd21549
SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif ...
 3489-3629 8.51e-21

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439212  Cd Length: 164  Bit Score: 91.88  E-value: 8.51e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3489 WQGLLALKNDTAAVQLHFVSGNNVLAHRSL-PLSEGG--PPLRIAQRMRLEASQLEGVARRMTVE--TDYCLLLALPCGR 3563
Cdd:cd21549     2 WQGMLLLKNSNFPSNMHLLEGDLSVASSLLvDGSTGGkvAQLKITQRLRLDQPKLDEVTRRIKVAgpNGYAVLLAVPGSS 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674 3564 DQEDVVSQTESLKAAF---ITYLQAKQAAGIINVPNPGSNQP--AYVLQIFPPCEFSESHLSRLAPDLLAS 3629
Cdd:cd21549    82 EVSSVSDQATSTQRPLrnlVSYLKQKQAAGVISLPVGGSKDKdnTGVLHAFPPCDFSQQFLDSSAKALAKS 152
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
 438-514 8.35e-18

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 80.52  E-value: 8.35e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKV--NGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12309     1 ATRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPprGQGNAYAFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGYGK 79
RRM smart00360
RNA recognition motif;
441-510 7.97e-15

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 71.86  E-value: 7.97e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLvrDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 339-594 9.06e-15

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 80.62  E-value: 9.06e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   339 IKVQNLPvRSTDTSlkdGLFHEFKKFGKVTSVQIhgASEER-----YGLVFFRQQEDQEKALTASKGKLFFGMQIevtaW 413
Cdd:TIGR01628   91 IFVKNLD-KSVDNK---ALFDTFSKFGNILSCKV--ATDENgksrgYGFVHFEKEESAKAAIQKVNGMLLNDKEV----Y 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   414 VGPeteseneFRPLDERIDEFHPKATrTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQYAFLQYCDIASV 491
Cdd:TIGR01628  161 VGR-------FIKKHEREAAPLKKFT-NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKdgSGRSRGFAFVNFEKHEDA 232

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   492 CKAIKKMDGEYLGN----NRLKLG-----------------------FGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGP 544
Cdd:TIGR01628  233 AKAVEEMNGKKIGLakegKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGE 311

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 568931674   545 VV--KVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQ 594
Cdd:TIGR01628  312 ITsaKVMLDekgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ 366
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 442-510 1.09e-14

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 71.16  E-value: 1.09e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIvRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 8-75 2.97e-14

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 70.00  E-value: 2.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNgtELGGRPLK 70
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
 437-517 3.31e-14

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 70.65  E-value: 3.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  437 KATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVN--GVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12555     5 RANRTLFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGrgQTSTYGFLKFENLDMAHRAKLAMSGKVIGRNPIKIGYGK 84


                  ...
gi 568931674  515 SMP 517
Cdd:cd12555    85 ATP 87
SPOC_RBM15B cd21550
SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein ...
 3488-3641 4.03e-14

SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein 15B (RBM15B); RBM15B, also called one-twenty two 3 (OTT3), is a paralog of RNA binding motif protein 15 (RBM15), which is also known as one-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which contains a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439213  Cd Length: 167  Bit Score: 72.97  E-value: 4.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3488 VWQGLLALKNDTAAVQLHFVSGNNVLAHRSLP-LSEGG--PPLRIAQRMRLEASQLEGVARRMTVET--DYCLLLAL--- 3559
Cdd:cd21550     1 AWNGVLVLKNSCFPTNMHILEGDLGVVNILLKdYTSGGklTQLKIAQRLRLDQPKLDEVTRRIKQGSpdGYAVLLATqap 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3560 PCGRDQEDVVSQ---TESLKAAFITYLQAKQAAGIINVPNPGSNQ--PAYVLQIFPPCEFSESHLsRLAPDLLASISniS 3634
Cdd:cd21550    81 QGGEGGGAPPVEpglQRRLLRNLVSYLKQKQAAGVISLPVGGSKDrdNTGMLYAFPPCDFSQQYL-QSALRTLGKLE--E 157


                  ....*..
gi 568931674 3635 PHLMIVI 3641
Cdd:cd21550   158 EHMVIVI 164
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 521-587 7.15e-13

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 66.15  E-value: 7.15e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVF-----DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVD 587
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIvrdrdGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM smart00360
RNA recognition motif;
8-75 9.41e-13

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 65.69  E-value: 9.41e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674      8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGfAFVEFESEEDAEKALEALNgkELDGRPLK 72
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 357-583 9.60e-13

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 74.07  E-value: 9.60e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   357 LFHEFKKFGKVTSVQIHGASEER----YGLVFFRQQEDQEKALTASKGKLFFGMQIEVtAWVgpetesenefrpldERID 432
Cdd:TIGR01628   17 LYDLFKPFGPVLSVRVCRDSVTRrslgYGYVNFQNPADAERALETMNFKRLGGKPIRI-MWS--------------QRDP 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   433 EFHPKATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:TIGR01628   82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVaTDENGKSRgYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   511 gfGKSMP------------TNcVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRL-----KGMALVLYSEIEDAQAAVKE 573
Cdd:TIGR01628  162 --GRFIKkhereaaplkkfTN-LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDgsgrsRGFAFVNFEKHEDAAKAVEE 238

                          250
                   ....*....|
gi 568931674   574 TKGRKIGGNK 583
Cdd:TIGR01628  239 MNGKKIGLAK 248
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 442-509 4.69e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 63.79  E-value: 4.69e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLvRDETGRSKgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
520-586 1.39e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 62.61  E-value: 1.39e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    520 CVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVesVRLVRDketgKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 8-75 6.24e-11

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 60.71  E-value: 6.24e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674     8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNgkELGGRELK 70
RRM1_Spen cd12308
RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily ...
 339-413 7.76e-11

RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family; This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also known as one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong- to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409749 [Multi-domain]  Cd Length: 78  Bit Score: 60.72  E-value: 7.76e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  339 IKVQNLPVRSTDTSLKDGLFHEFKKFGKVtSVQIHGASEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVTAW 413
Cdd:cd12308     4 LCVSNLPAKLSDEEIEDVLYHEFKKFGDV-SVRLQHDGDERVAYVNFRHPEDAREAKHAKLRLVLFDRPLNVEPV 77
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1629-2063 1.08e-10

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 68.43  E-value: 1.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1629 PETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAgekPAEPAPVSEETKLVSEPASV 1708
Cdd:PHA03247 2571 PRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP---PPSPSPAANEPDPHPPPTVP 2647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1709 PVEQPRQSDVPPgedsRDSQDSAALAPSAPQESAATDAVPCVNAEPltpgTTVSQVESSVDPKP------SSPQPLSKLT 1782
Cdd:PHA03247 2648 PPERPRDDPAPG----RVSRPRRARRLGRAAQASSPPQRPRRRAAR----PTVGSLTSLADPPPppptpePAPHALVSAT 2719

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1783 QRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA-QPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVtr 1861
Cdd:PHA03247 2720 PLPPGPAAARQASPALPAAPAPPAVPAGPATPGGpARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRES-- 2797

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1862 kseridreklkrSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTehPEPSLPLSRSRRRNVRSVYATMT-------DHE 1934
Cdd:PHA03247 2798 ------------LPSPWDPADPPAAVLAPAAALPPAASPAGPLPP--PTSAQPTAPPPPPGPPPPSLPLGgsvapggDVR 2863

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1935 SRSPAKEPVEQP---------RVTRKRLERELQEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSPRS 2005
Cdd:PHA03247 2864 RRPPSRSPAAKPaaparppvrRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674 2006 QKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPST 2063
Cdd:PHA03247 2944 APTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSL 3001
RRM1_RBM15 cd12553
RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
 339-402 2.45e-10

RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM1 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409969 [Multi-domain]  Cd Length: 78  Bit Score: 59.19  E-value: 2.45e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  339 IKVQNLPVRSTDTSLKDGLFHEFKKFGKVtSVQIHGASEERYGLVFFRQQEDQeKALTASKGKL 402
Cdd:cd12553     4 LKISELGSQLSDEAVEDGLFHEFKKFGDV-SVKISRLGDERVAFVNFRRPEDA-RAAKHARGRL 65
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
 441-513 4.25e-10

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 58.10  E-value: 4.25e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 513
Cdd:cd12346     3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGC---GFVQFVNRASAEAAIQKLQGTPIGGSRIRLSWG 72
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
 437-514 4.54e-10

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 58.77  E-value: 4.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  437 KATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvNGVPQ---YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 513
Cdd:cd12556     6 RATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKR-PARGQggaYAFLKFQNLDMAHRAKVAMSGRVIGRNPIKIGYG 84


                  .
gi 568931674  514 K 514
Cdd:cd12556    85 K 85
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 5-78 7.54e-10

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 57.79  E-value: 7.54e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSeggvaAFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12262     3 SRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNC-----AFVNYLNIANAIKAVQELPikNPKFKKVRINY 73
PTZ00121 PTZ00121
MAEBL; Provisional
 635-1272 7.98e-10

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 65.55  E-value: 7.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  635 AQSPHKCREERRgsyeySQERTYYENVRTPgtypEDSRRDYPARGREFYSEWETYQGEYYDSRYYDEPREYREYRSDPyE 714
Cdd:PTZ00121 1190 AEELRKAEDARK-----AEAARKAEEERKA----EEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFE-E 1259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  715 QDIREYSYRQRERERERERFESD--------------RDHERRPIERSQSPVHLRRPQSPGVSPAHSERLPSDSERRLYR 780
Cdd:PTZ00121 1260 ARMAHFARRQAAIKAEEARKADElkkaeekkkadeakKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAE 1339

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  781 RSSERSGSCSSVSPPRYDKLEKARlerytKNEKADKERTfdpERVERERRIVRKEKGEKDKAERQKRKGKAHSPSSQPSE 860
Cdd:PTZ00121 1340 EAKKAAEAAKAEAEAAADEAEAAE-----EKAEAAEKKK---EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELK 1411

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  861 TEQENDREQSPEKPRGSTKLSRDRADKEGPAKNRLELVpcvvltRVKEKEGKVIEHPPP---EKLKA-RLGRDTTKASAL 936
Cdd:PTZ00121 1412 KAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEA------KKKAEEAKKAEEAKKkaeEAKKAdEAKKKAEEAKKA 1485

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  937 DQKPQAAQGEPAKSDPARGKALREKVLPSHAEVGEKEGRTKLRKHLKAEQTPELSALDlEKLEARKRRFADSGLKIE-KQ 1015
Cdd:PTZ00121 1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAE-EKKKADELKKAEELKKAEeKK 1564

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1016 KPEIKKTSPETEDT---RILLKKQPDTSRDGVLLREGESERKPVRKEILKRESKKTKLERLNSALSPKDCQDPAAVSAGS 1092
Cdd:PTZ00121 1565 KAEEAKKAEEDKNMalrKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAE 1644

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1093 GSRPSSDVHAglgelthgsvETQETQPKKAIPSKPQPKQLQLLENQGPEKEEVRKNYCRPREEPAEHRAGQEKPHGGNAE 1172
Cdd:PTZ00121 1645 EKKKAEELKK----------AEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEE 1714

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1173 EKLGIDIDHTQSYRK-QMEQSRRKQrmEMEIAKAEKFgspkkDVDDYERRSLVHEVGKPPQDVTDDSPPSKKRRTDHVDF 1251
Cdd:PTZ00121 1715 KKKAEELKKAEEENKiKAEEAKKEA--EEDKKKAEEA-----KKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDE 1787

                         650       660
                  ....*....|....*....|.
gi 568931674 1252 DICTKRERNYRSSRQISEDSE 1272
Cdd:PTZ00121 1788 EDEKRRMEVDKKIKDIFDNFA 1808
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
 518-589 1.45e-09

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 56.85  E-value: 1.45e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  518 TNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12363     1 SRCLGVFGLSLYTTERDLREVFSRYGPIekVQVVYDqqtgRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRVDYS 78
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
 525-589 3.59e-09

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 55.95  E-value: 3.59e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  525 GLSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12449     7 GLSFDTNEQSLEEVFSKYGQISEVVVvkdretQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQA 77
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 519-589 8.35e-09

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 54.83  E-value: 8.35e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  519 NCVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12398     1 RSVFVGNIPYDATEEQLKEIFSEVGPVVsfRLVTDRetgkPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
 521-589 1.22e-08

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 54.36  E-value: 1.22e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12447     2 LFVGGLSWNVDDPWLKKEFEKYGGVIsaRVITDRGsgrsKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 339-410 1.35e-08

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 53.83  E-value: 1.35e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  339 IKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQIHGASEER---YGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:cd00590     1 LFVGNLPPDTTEEDLRE----LFSKFGEVVSVRIVRDRDGKskgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
 441-512 1.60e-08

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 53.91  E-value: 1.60e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12338     1 RIYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRRRGPPFAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
PTZ00121 PTZ00121
MAEBL; Provisional
 669-1320 1.72e-08

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 60.93  E-value: 1.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  669 EDSRRDYPAR-GREFYSEWETYQGEyyDSRYYDEPREYREYRSdpyEQDIREYSYRQRERERERERFESDRDHERRPIER 747
Cdd:PTZ00121 1173 EDAKKAEAARkAEEVRKAEELRKAE--DARKAEAARKAEEERK---AEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEE 1247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  748 SQSPVHLRRPQSPGVSPAHSERLPSDSERRLYRRSSERSGSCSSVSPPRYDKLEKARLERYTKNEKADK-ERTFDPERVE 826
Cdd:PTZ00121 1248 ERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKaDEAKKKAEEA 1327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  827 RERRIVRKEKGE--KDKAERQKRKGKAHSPSSQPSETEQENDREQSPEKPRGSTKLSR--DRADKEGPAKNRLELVPcvv 902
Cdd:PTZ00121 1328 KKKADAAKKKAEeaKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKkaEEKKKADEAKKKAEEDK--- 1404

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  903 lTRVKEKEGKVIEHPPPEKLKARlGRDTTKASALDQKPQaaqgEPAKSDPARGKAlREKVLPSHAEVGEKEGRTKLRKHL 982
Cdd:PTZ00121 1405 -KKADELKKAAAAKKKADEAKKK-AEEKKKADEAKKKAE----EAKKADEAKKKA-EEAKKAEEAKKKAEEAKKADEAKK 1477

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  983 KAEQTPELSALDLEKLEARKRrfADSGLKIEKQKPEIKKTSPETEDTRILLKKQPDTSRDGVLLREGESERKP--VRK-E 1059
Cdd:PTZ00121 1478 KAEEAKKADEAKKKAEEAKKK--ADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKAdeLKKaE 1555

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1060 ILKRESKKTKLERLNSALSPKDCQDPAAVSAGSGSRPSSDVHAGLGElthGSVETQETQPKKAIPSKPQPKQLQLLEN-- 1137
Cdd:PTZ00121 1556 ELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYE---EEKKMKAEEAKKAEEAKIKAEELKKAEEek 1632

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1138 ------QGPEKEEVRK-NYCRPREEPAEHRAGQEKPhggNAEEklgiDIDHTQSYRKQMEQSRRK----QRMEMEIAKAE 1206
Cdd:PTZ00121 1633 kkveqlKKKEAEEKKKaEELKKAEEENKIKAAEEAK---KAEE----DKKKAEEAKKAEEDEKKAaealKKEAEEAKKAE 1705

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1207 KFgspKKDVDDYERRSlvHEVGKPPQDVTDDSPPSKKrrtdhvdfdictKRERNYRSSRQISEDSERTSCSPSVRHGSFH 1286
Cdd:PTZ00121 1706 EL---KKKEAEEKKKA--EELKKAEEENKIKAEEAKK------------EAEEDKKKAEEAKKDEEEKKKIAHLKKEEEK 1768

                         650       660       670
                  ....*....|....*....|....*....|....
gi 568931674 1287 DDDDPRGSPRLVSVKGSPKGDEKGLPYPNAAVRD 1320
Cdd:PTZ00121 1769 KAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKD 1802
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 10-75 1.83e-08

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 53.66  E-value: 1.83e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674   10 VGNLPENVREEKIIEHFKRYGRVESVKILpkRGSEGGVA---AFVDFVDIKSAQKA---HNSvnKMGDRDLR 75
Cdd:cd12395     4 VGNLPFDIEEEELRKHFEDCGDVEAVRIV--RDRETGIGkgfGYVLFKDKDSVDLAlklNGS--KLRGRKLR 71
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
 521-590 2.34e-08

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 53.44  E-value: 2.34e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGN--KIKVDFAN 590
Cdd:cd12310     1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGPdrRLRVDFAD 72
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
 441-515 2.86e-08

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 53.43  E-value: 2.86e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKS 515
Cdd:cd12235     5 VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVirdKKTGDSLQYAFIEFETKESCEEAYFKMDNVLIDDRRIHVDFSQS 82
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 525-589 3.53e-08

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 52.94  E-value: 3.53e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  525 GLSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd21608     6 NLSWDTTEDDLRDLFSEFGEVesAKVITDREtgrsRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 526-589 3.57e-08

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 52.94  E-value: 3.57e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  526 LSSNVSDQYLTRHFCRYGPVVKVVF-----DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12414     7 LPFKCTEDDLKKLFSKFGKVLEVTIpkkpdGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
 5-75 3.72e-08

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 52.91  E-value: 3.72e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKI------LPKRGSEGGvaaFVDFVDIKSAQKAHNSVNKM--GDRDLR 75
Cdd:cd21619     1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVRRppihtdKADRTTGFG---FIKYTDAESAERAMQQADGIllGRRRLV 76
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 526-588 3.82e-08

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 53.39  E-value: 3.82e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 588
Cdd:cd12236     9 LSYDTTESKLRREFEKYGPIkrVRLVRDKKtgksRGYAFIEFEHERDMKAAYKHADGKKIDGRRVLVDV 77
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2949-3474 5.87e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.57  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2949 PANLGPTLTPHHPPALP------------SKLPAEVNHVPSGPSTPADRTIAHLATPKPDTHSPRPTGPT-------PGL 3009
Cdd:PHA03247 2512 PSRLAPAILPDEPVGEPvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAvtsrarrPDA 2591

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3010 FPRPCHPSSTTSTALSTNATVMLAAGIPVPqfissiHPEQSVIMPPHSITQTVSLGHLSQGEVRMSTPTLPSITYSIRPE 3089
Cdd:PHA03247 2592 PPQSARPRAPVDDRGDPRGPAPPSPLPPDT------HAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR 2665

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3090 TLHSPRAPLQPQQiEARAPQRVGTPqPATTGVPALATQHPPEEEVHyhlPVARAAAPVQSEVLVMQSEYRLHPYT----- 3164
Cdd:PHA03247 2666 RARRLGRAAQASS-PPQRPRRRAAR-PTVGSLTSLADPPPPPPTPE---PAPHALVSATPLPPGPAAARQASPALpaapa 2740

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3165 ---------VPRDVRIMVHPHVTAVSEQPRATEGVVKVPPANKAPQQLVKEAVKTSDAKAVPAPAPVPVPVPVPTPAPPP 3235
Cdd:PHA03247 2741 ppavpagpaTPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPP 2820

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3236 HGEARILTVTPSSQLQGLPLTPPVVVTHGVQIVHSSGELFQEYRYGDVRTyhAPAQQLTHTQFPVASSISLA-SRTKTSA 3314
Cdd:PHA03247 2821 AASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS--PAAKPAAPARPPVRRLARPAvSRSTESF 2898

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3315 QVPPEGEPLQSTQSAQPAPSTQATqpiPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEP 3394
Cdd:PHA03247 2899 ALPPDQPERPPQPQAPPPPQPQPQ---PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3395 HAQL--QRAPVETAQPAHPSPVSVSMkPDLPSPLSSQA----------APKQPLFVPANSGPSTPPGLALPHAE------ 3456
Cdd:PHA03247 2976 RFRVpqPAPSREAPASSTPPLTGHSL-SRVSSWASSLAlheetdpppvSLKQTLWPPDDTEDSDADSLFDSDSErsdlea 3054

                         570
                  ....*....|....*...
gi 568931674 3457 VQPAPKQESSPHGTPQRP 3474
Cdd:PHA03247 3055 LDPLPPEPHDPFAHEPDP 3072
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
 5-62 8.25e-08

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 52.05  E-value: 8.25e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGseggvAAFVDFVDIKSAQKA 62
Cdd:cd12523     3 SRNVYLGNLPESITEEELREDLEKFGPIDQIKIVKEKN-----IAFVHFLSIANAIKV 55
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 439-515 1.08e-07

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 51.91  E-value: 1.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--------KKVNGVPqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12223     1 TTNLYVGNLPPSVTEEVLLREFGRFGPLASVKImwprteeeRRRNRNC--GFVAFMSRADAERAMRELNGKDVMGYELKL 78


                  ....*
gi 568931674  511 GFGKS 515
Cdd:cd12223    79 GWGKA 83
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 438-514 1.52e-07

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 51.24  E-value: 1.52e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12262     2 ASRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNC---AFVNYLNIANAIKAVQELPIKNPKFKKVRINYGK 75
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
 521-591 1.69e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 51.09  E-value: 1.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKV-VFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 591
Cdd:cd12373     2 VYVGNLGPRVTKRELEDAFEKYGPLRNVwVARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 438-510 1.79e-07

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 50.90  E-value: 1.79e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12227     1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGC---AYVCMKTRQDAHRALQKLKNHKLRGKSIKI 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 329-533 1.86e-07

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 56.85  E-value: 1.86e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   329 EKDEPRKSFGIKVQNLPVRSTDTSLKDglFheFKKFGKVTSVQIHGASEER----YGLVFFRQQEDQEKALTASkGKLFF 404
Cdd:TIGR01622  107 LTEDERDRRTVFVQQLAARARERDLYE--F--FSKVGKVRDVQIIKDRNSRrskgVGYVEFYDVDSVQAALALT-GQKLL 181

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   405 GMQIEVTAwvgpeTESE-NEFRPLDERIDEFHPKAT--RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ-- 479
Cdd:TIGR01622  182 GIPVIVQL-----SEAEkNRAARAATETSGHHPNSIpfHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRsk 256

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674   480 -YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG-KSMPTNCVWLDGLSSNVSDQ 533
Cdd:TIGR01622  257 gYGFIQFRDAEQAKEALEKMNGFELAGRPIKVGLGnDFTPESDANLAQRFQDQDGS 312
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 525-591 2.35e-07

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 50.67  E-value: 2.35e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  525 GLSSNVSDQYLTRHFCRYGPVvKVVF-------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 591
Cdd:cd12413     6 NLPYDTTDEQLEELFSDVGPV-KRCFvvkdkgkDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKK 78
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 521-589 2.68e-07

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 50.69  E-value: 2.68e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12324     9 IFVTGVHEEAQEEDIHDKFAEFGEIknLHLNLDRrtgfVKGYALVEYETKKEAQAAIEGLNGKELLGQTISVDWA 83
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
 442-508 2.85e-07

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 50.49  E-value: 2.85e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGV---PQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12229     6 LFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGgrlPNFGFVVFDDPEAVQKILANKPIMFRGEHRL 75
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
 8-80 3.24e-07

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 50.13  E-value: 3.24e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKI--LPKRGSEGGVaAFVDFVDIKSAQKA--HNSVNKMGDRDLRTDYNE 80
Cdd:cd12397     1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMatFEDSGKCKGF-AFVDFKEIESATNAvkGPINHSLNGRDLRVEYGE 76
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
 440-509 3.27e-07

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 50.41  E-value: 3.27e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12392     3 NKLFVKGLPFSCTKEELEELFKQHGTVKDVRLvTYRNGKPKgLAYVEYENEADASQAVLKTDGTEIKDHTIS 74
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 6-78 3.40e-07

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 50.21  E-value: 3.40e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKR--GSEGGVaAFVDFVDIKSAQKAHNSVNK--MGDRDLRTDY 78
Cdd:cd12398     1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDRetGKPKGY-GFCEFRDAETALSAVRNLNGyeLNGRPLRVDF 76
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 8-77 3.96e-07

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 50.09  E-value: 3.96e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGsEGGVAAF--VDFVDIKSAQKAHNSVNK-MGDRDLRTD 77
Cdd:cd12450     2 LFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRD-DGRSKGFghVEFASAESAQKALEKSGQdLGGREIRLD 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
8-75 3.97e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 50.10  E-value: 3.97e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRgsEGGVA---AFVDFVDIKSAQKAHNSVN--KMGDRDLR 75
Cdd:COG0724     4 IYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDR--ETGRSrgfGFVEMPDDEEAQAAIEALNgaELMGRTLK 74
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 441-513 4.73e-07

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 49.59  E-value: 4.73e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 513
Cdd:cd12354     2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPDKG---YAFIRFDSHEAATHAIVSVNGTIINGQAVKCSWG 71
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 521-585 4.85e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 4.85e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   521 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIK 585
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIksIRLVRDetgRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
339-410 6.64e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.13  E-value: 6.64e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    339 IKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQI-----HGASeERYGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:smart00360    2 LFVGNLPPDTTEEELRE----LFSKFGKVESVRLvrdkeTGKS-KGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
 517-589 6.75e-07

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 49.60  E-value: 6.75e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  517 PTNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12642     3 PNTCLGVFGLSLYTTERDLREVFSRYGPLagVNVVYDqrtgRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYS 81
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
 440-514 8.60e-07

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 48.82  E-value: 8.60e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIkkvngVP--QYAFLQYCDIASVCKAIKKMDGE-YLGNNRLKLGFGK 514
Cdd:cd12224     2 TTLYVGGLGDKITEKDLRDHFYQFGEIRSITV-----VArqQCAFVQFTTRQAAERAAERTFNKlIIKGRRLKVKWGR 74
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 5-75 9.45e-07

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 48.97  E-value: 9.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEggvaafvdFVDIKSAQKAHNSVNKMGDRDLR 75
Cdd:cd12227     2 STTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCA--------YVCMKTRQDAHRALQKLKNHKLR 64
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
 439-485 1.09e-06

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 49.01  E-value: 1.09e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDID-IKKVNGVPQYAFLQY 485
Cdd:cd12454     3 KLSIFVGQLDPKTTDSELFRRFSKYGKIVDCKlIKRPEPVNAFAFLRF 50
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 535-589 1.16e-06

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 48.60  E-value: 1.16e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  535 LTRHFCRYGPVVKVvfDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12233    17 IEKLFEPFGPLVRC--DIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFV 69
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
 442-509 1.40e-06

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 48.38  E-value: 1.40e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIV------DIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12362     1 LFVYHLPNEFTDQDLYQLFAPFGNVVsakvfvDKNTGRSKG---FGFVSYDNPLSAQAAIKAMNGFQVGGKRLK 71
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
 8-62 1.41e-06

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 48.42  E-value: 1.41e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIL------PKRGseggvAAFVDFVDIKSAQKA 62
Cdd:cd12328     2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIVtdketgKKRG-----FAFVTFDDHDSVDKI 57
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
 8-72 1.51e-06

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 48.37  E-value: 1.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRG---SEGgvAAFVDFVDIKSAQKA---HNSvnKMGDR 72
Cdd:cd12400     3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDKKtgkSKG--CAFVEFDNQKALQKAlklHHT--SLGGR 69
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 8-65 1.64e-06

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 47.94  E-value: 1.64e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674    8 LWVGNLP-ENVREEKIIEHFKRYGRVESVKILPKRGSeggvaAFVDFVDIKSAQKAHNS 65
Cdd:cd12257     4 LEVRNIPpELNNITKLREHFSKFGTIVNIQVNYNPES-----ALVQFSTSEEANKAYRS 57
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
 521-589 1.66e-06

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 48.55  E-value: 1.66e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12382     4 LFIGGLNTETNEKALEAVFGKYGRIVEVLLmkdretNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQA 78
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
 8-78 1.97e-06

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 241042 [Multi-domain]  Cd Length: 72  Bit Score: 47.87  E-value: 1.97e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGgvAAFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12598     2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVP--FAFVRFEDPRDAEDAVFGRNgyDFGQCRLRVEF 72
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 5-67 2.17e-06

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 48.06  E-value: 2.17e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSE----GGVAAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12223     1 TTNLYVGNLPPSVTEEVLLREFGRFGPLASVKIMWPRTEEerrrNRNCGFVAFMSRADAERAMRELN 67
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 441-510 2.30e-06

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 47.99  E-value: 2.30e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ----YAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12318     2 TLFVKNLNFKTTEEALKKHFEKCGPIRSVTIakKKDPKGPLlsmgYGFVEFKSPEAAQKALKQLQGTVLDGHALEL 77
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
 5-62 2.42e-06

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 47.78  E-value: 2.42e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12309     2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRA 59
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 442-508 2.46e-06

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 47.63  E-value: 2.46e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12417     2 LWISGLSDTTKAADLKKIFSKYGKVVSAKVvtsARTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVI 71
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 442-513 2.55e-06

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 47.62  E-value: 2.55e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFG 513
Cdd:cd12284     1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQKdpETGRSKgYGFIQFRDAEDAKKALEQLNGFELAGRPMKVGHV 75
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
 442-508 2.74e-06

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 47.49  E-value: 2.74e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12608     3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVMK-----QFAFVHMRGEAAADRAIRELNGRELHGRAL 64
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 440-508 3.03e-06

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 47.64  E-value: 3.03e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---------KKVNGvpqYAFLQYCDIASVCKAIkKMDGEYLGNNRL 508
Cdd:cd12298     1 REIRVRNLDFELDEEALRGIFEKFGEIESINIpkkqknrkgRHNNG---FAFVTFEDADSAESAL-QLNGTLLDNRKI 74
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 8-69 3.03e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 47.86  E-value: 3.03e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVR-EEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKM 69
Cdd:cd12675     3 LIIRNLPWSIKkPVHLKKLFGRYGKVVEATIPRKKGGKLSGFAFVTMKGRKNAEEALESVNGL 65
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
 539-586 3.15e-06

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 47.28  E-value: 3.15e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568931674  539 FCRYGPVVKV--VFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12393    22 FSKYGKVVKVtiLKDKEtrksKGVAFVLFLDRESAHNAVRAMNNKELFGRTLKC 75
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
 8-69 3.29e-06

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 47.28  E-value: 3.29e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGseggvAAFVDFVDIKSAQKA-HNSVNKM 69
Cdd:cd12224     4 LYVGGLGDKITEKDLRDHFYQFGEIRSITVVARQQ-----CAFVQFTTRQAAERAaERTFNKL 61
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 526-590 3.48e-06

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 47.40  E-value: 3.48e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  526 LSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVkETKGRKIGGNKIKVDFAN 590
Cdd:cd12450     7 LSWSATQDDLENFFSDCGEVVDVRIamdrddGRSKGFGHVEFASAESAQKAL-EKSGQDLGGREIRLDLAN 76
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 8-78 3.55e-06

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 47.16  E-value: 3.55e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12414     2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNgkKIKGRPVAVDW 74
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
 442-503 3.61e-06

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 47.16  E-value: 3.61e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDID--IKKVNGVP-QYAFLQYCDIASVCKAIKKMDGEYL 503
Cdd:cd12365     1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDlpIDREPNLPrGYAYVEFESPEDAEKAIKHMDGGQI 65
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 8-62 3.65e-06

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 47.16  E-value: 3.65e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKR--G-SEGgvAAFVDFVDIKSAQKA 62
Cdd:cd21608     2 LYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDRetGrSRG--FGFVTFSTAEAAEAA 57
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
 527-589 3.95e-06

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 47.27  E-value: 3.95e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  527 SSNVSDQYLTRHFCRYGPVvKVVFDRLK--GMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12524    10 NSSVEDEELRALFEQFGEI-RTLYTACKhrGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFS 73
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
 526-589 4.05e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 47.05  E-value: 4.05e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  526 LSSNVSDQYLTRHFCRYGPVVKV---VFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12397     6 LSFETTEEDLRKHFAPAGKIRKVrmaTFEdsgKCKGFAFVDFKEIESATNAVKGPINHSLNGRDLRVEYG 75
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
 517-589 4.41e-06

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 47.31  E-value: 4.41e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  517 PTNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12641     6 PNCCLGVFGLSLYTTERDLREVFSKYGPIadVSIVYDqqsrRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 84
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
 439-517 4.66e-06

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 46.89  E-value: 4.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDI-DIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFgkSMP 517
Cdd:cd12524     1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLyTACKHRG---FIMVSYYDIRAAQSAKRALQGTELGGRKLDIHF--SIP 75
RRM4_MRN1 cd12522
RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This ...
 438-514 5.00e-06

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409942 [Multi-domain]  Cd Length: 81  Bit Score: 47.14  E-value: 5.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  438 ATRTLFIGNLE--KTTTYHDLRNIFQRFGEivdidIKKVNGVPQY--AFLQYCDIASVCKAIKKMDGEYlGNNRLKLGFG 513
Cdd:cd12522     2 ASRNVYIGNIDdvRVLTEERLRHDFSQYGE-----IEQVNFLREKncAFVNFTNIANAIKAIDKIKSKP-YYKDLKINFG 75


                  .
gi 568931674  514 K 514
Cdd:cd12522    76 K 76
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 8-68 5.12e-06

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 46.91  E-value: 5.12e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIL-----PKRGSEGGVaAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12355     2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLfhktgPLKGQPRGY-CFVTFETKEEAEKAIECLNG 66
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
 8-67 5.34e-06

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 46.66  E-value: 5.34e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12614     1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQTLN 60
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
 3-62 5.69e-06

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 47.22  E-value: 5.69e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    3 RETRHLWVGNLPENVREEKIIEHFKRYGRVESVKI-LPKRGsEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12556     6 RATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIkRPARG-QGGAYAFLKFQNLDMAHRA 65
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
 439-594 6.42e-06

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 51.48  E-value: 6.42e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   439 TRTLFIGN-LEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVP-QYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:TIGR01661    2 SKTNLIVNyLPQTMTQEEIRSLFTSIGEIESCKLvrDKVTGQSlGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   515 ----SMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKV------VFDRLKGMALVLYSEIEDAQAAVKETKGRKIGG--N 582
Cdd:TIGR01661   82 pssdSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSrilsdnVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGctE 161

                          170
                   ....*....|..
gi 568931674   583 KIKVDFANRESQ 594
Cdd:TIGR01661  162 PITVKFANNPSS 173
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
 442-509 7.14e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 46.07  E-value: 7.14e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12343     2 IFVGNLPDAATSEELRALFEKYGKVTECDIVK-----NYAFVHMEKEEDAEDAIKALNGYEFMGSRIN 64
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
 442-509 8.29e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 46.11  E-value: 8.29e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ---YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12311     1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTREsrgFAFVRFYDKRDAEDAIDAMDGAELDGRELR 71
RRM1_SRSF1 cd12597
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
 442-512 9.72e-06

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 410010 [Multi-domain]  Cd Length: 79  Bit Score: 46.38  E-value: 9.72e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12597     7 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 77
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 442-508 9.78e-06

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 46.14  E-value: 9.78e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ------YAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12355     2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFHKTGPLkgqprgYCFVTFETKEEAEKAIECLNGKLALGKKL 74
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
 432-571 1.18e-05

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 50.79  E-value: 1.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   432 DEFHPKATRTLFIGN-LEKTTTYHDLRNIFQRFGEIVDIDIK---KVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNR 507
Cdd:TIGR01659   99 DDNDTNNSGTNLIVNyLPQDMTDRELYALFRTIGPINTCRIMrdyKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR 178

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674   508 LKLGF----GKSMPTNCVWLDGLSSNVSDQYLTRHFCRYGPVVK--VVFDRL----KGMALVLYSEIEDAQAAV 571
Cdd:TIGR01659  179 LKVSYarpgGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQknILRDKLtgtpRGVAFVRFNKREEAQEAI 252
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 526-593 1.22e-05

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 46.03  E-value: 1.22e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  526 LSSNVSDQYLTRHFCRYGPVVK-VVFDRLKGM-ALVLYSEIEDAQAAVKETKGRKI--GGNKIKVDFANRES 593
Cdd:cd12422     9 LLYPVTVDVLHQVFSPYGAVEKiVIFEKGTGVqALVQFDSVESAEAAKKALNGRNIydGCCTLDIQFSRLKE 80
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
 526-591 1.23e-05

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 45.72  E-value: 1.23e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 591
Cdd:cd12381     9 LDDTIDDEKLREEFSPFGTItsAKVMTDeggRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
439-509 1.24e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.86  E-value: 1.24e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLItdRETGRSRgFGFVEMPDDEEAQAAIEALNGAELMGRTLK 74
RRM_TUT1 cd12279
RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase ...
 519-586 1.28e-05

RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).


Pssm-ID: 409721 [Multi-domain]  Cd Length: 74  Bit Score: 45.49  E-value: 1.28e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  519 NCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGM-ALVLYSEIEDAQAAVKETKgRKIGGNKIKV 586
Cdd:cd12279     3 RSVFVSGFKRGTSELELSDYFQAFGPVASVVMDKDKGVyAIVEMDSTETVEKVLSQPQ-HCLNGQRLRV 70
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
 8-62 1.40e-05

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 45.87  E-value: 1.40e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKA 62
Cdd:cd12229     6 LFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGGRLPNfGFVVFDDPEAVQKI 61
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
 6-78 1.42e-05

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 46.92  E-value: 1.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILpkRGSEGGVA---AFVDFVDIKSAQKAHNSVN-----KMGDRDLRTD 77
Cdd:cd21615    19 KTLFVGRLDYSLTELELQKKFSKFGEIEKIRIV--RDKETGKSrgyAFIVFKSESDAKNAFKEGNglrglKINDRTCIVD 96


                  .
gi 568931674   78 Y 78
Cdd:cd21615    97 I 97
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
 8-65 1.56e-05

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 45.69  E-value: 1.56e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYgrvESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNS 65
Cdd:cd12245     5 LFVANLGPNVSEQELRQLFSRQ---PGFRRLRMHNKGGGPVCFVEFEDVPFATQALNH 59
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 8-74 1.67e-05

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 45.20  E-value: 1.67e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSE--GGVAafvdFVDIKSAQKAHNSVNKMGDRDL 74
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDRETKrpRGFG----FVELQEEESAEKAIAKLDGTDF 65
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
 440-509 1.81e-05

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 45.76  E-value: 1.81e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVP-QYAFLQYCDIASVCKAIkKMDGEYLGNNRLK 509
Cdd:cd12260     5 RTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDETQPtRYAFVEFAEQTSVINAL-KLNGKMFGGRPLK 74
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
 517-591 1.85e-05

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 45.48  E-value: 1.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  517 PTNCVWLDGLSSNVSDQYL----TRHFCRYGPV--VKVVFDRL-KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12453     1 PSACLFVASLSSARSDEELcaavTNHFSKWGELlnVKVLKDWSnRPYAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKA 80


                  ....
gi 568931674  590 --NR 591
Cdd:cd12453    81 kvNR 84
RRM_SRSF3 cd12645
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); ...
 517-594 2.14e-05

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 241089 [Multi-domain]  Cd Length: 81  Bit Score: 45.42  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  517 PTNC-VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDR-LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQ 594
Cdd:cd12645     2 PLDCkVYVGNLGNNGNKTELERAFGYYGPLRSVWVARnPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 81
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
 8-67 2.15e-05

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 45.01  E-value: 2.15e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKI--LPKRGSEGGVaAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12290     2 VYVELLPKNATHEWIEAVFSKYGEVVYVSIprYKSTGDPKGF-AFIEFETSESAQKAVKHFN 62
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
 442-514 2.17e-05

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 44.97  E-value: 2.17e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNgvpQYAFLQYCDIASVCKAIKKMDGEYLGNN--RLKLGFGK 514
Cdd:cd12310     1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKGD---DYAYILYESLDAAQAAVRALRGFPLGGPdrRLRVDFAD 72
RRM3_RBM15B cd12558
RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from ...
 517-589 2.20e-05

RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409974 [Multi-domain]  Cd Length: 76  Bit Score: 45.00  E-value: 2.20e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  517 PTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGG--NKIKVDFA 589
Cdd:cd12558     1 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGFPLGGpdRRLRVDFA 75
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
 441-517 2.22e-05

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 45.78  E-value: 2.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDI----DIkkVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF--G 513
Cdd:cd12237     6 TLFVGRLSLQTTEEKLKEVFSRYGDIRRLrlvrDI--VTGFSKrYAFIEYKEERDALHAYRDAKKLVIDQYEIFVDFecE 83


                  ....
gi 568931674  514 KSMP 517
Cdd:cd12237    84 RTLP 87
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
 442-514 2.23e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 45.13  E-value: 2.23e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDI------DIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12397     1 LFVGNLSFETTEEDLRKHFAPAGKIRKVrmatfeDSGKCKG---FAFVDFKEIESATNAVKGPINHSLNGRDLRVEYGE 76
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 518-586 2.43e-05

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 44.86  E-value: 2.43e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  518 TNcVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12380     2 TN-VYVKNFGEDVDDDELKELFEKYGKItsAKVMKDdsgKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 442-500 2.64e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 44.85  E-value: 2.64e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDG 500
Cdd:cd12414     2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVTIpKKPDGKLRgFAFVQFTNVADAAKAIKGMNG 62
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
 8-62 2.67e-05

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 44.66  E-value: 2.67e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12338     2 IYVGNLPGDIRERDIEDLFYKYGPILAIDL--KNRRRGPPFAFVEFEDPRDAEDA 54
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
 441-501 2.71e-05

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 44.98  E-value: 2.71e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ-YAFLQYCDIASVCKAIKKMDGE 501
Cdd:cd21605     3 SIFVGNLPFDCTWEDLKDHFSQVGEVIRADIVTSRGRHRgMGTVEFTNKEDVDRAISKFDHT 64
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
 521-585 2.81e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 44.62  E-value: 2.81e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIK 585
Cdd:cd12346     4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKGCGFVQFVNRASAEAAIQKLQGTPIGGSRIR 68
RRM1_MRN1 cd12520
RNA recognition motif 1 (RRM1) found in RNA-binding protein MRN1 and similar proteins; This ...
 6-75 3.10e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM1 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa,which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240964 [Multi-domain]  Cd Length: 74  Bit Score: 44.74  E-value: 3.10e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674    6 RHLWVGNLPENVREEKIIEHFkRYGRVESVKILPKRgseggVAAFVDFVDIKSAQKAHNSVN----KMGDRDLR 75
Cdd:cd12520     2 RTVYLGNLPPNTTVKELLSHV-RSGPIENVRILPEK-----NCAFISFLDPSAATAFHSDAIlkrlSIKGVELK 69
RRM1_RBM34 cd12394
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 6-77 3.18e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409828 [Multi-domain]  Cd Length: 91  Bit Score: 44.89  E-value: 3.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKI---------LPKRG---------SEGGVAAFVDFVDIKSAQKA--HNS 65
Cdd:cd12394     1 RTVFVGNLPVTVKKKALKKLFKEFGKIESVRFrsvavanpkLPKKVavikkkfhpKRDSMNAYVVFKEEESAQKAlkLNG 80

                          90
                  ....*....|..
gi 568931674   66 vNKMGDRDLRTD 77
Cdd:cd12394    81 -TEFEGHHIRVD 91
rne PRK10811
ribonuclease E; Reviewed
 1620-1781 3.27e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 50.04  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1620 PKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAV-TVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAepAPVSEE 1698
Cdd:PRK10811  850 PQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVeAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIA--APVTEQ 927

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1699 TKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQ-----ESAATDAVPCVnAEPLTPGTTVSQVESSVDPKPS 1773
Cdd:PRK10811  928 PQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVvvaepEVVAQPAAPVV-AEVAAEVETVTAVEPEVAPAQV 1006


                  ....*...
gi 568931674 1774 SPQPLSKL 1781
Cdd:PRK10811 1007 PEATVEHN 1014
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2122-2642 3.40e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 3.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2122 EAGPAAASPqeSESPQKGSGSSPQLANNPADPDREAEEESASASTAPPEGTQLARQIElEQAVQNIAKLPEPSAAAASKG 2201
Cdd:PHA03247 2486 ARFPFAAGA--APDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLTWIRGLE-ELASDDAGDPPPPLPPAAPPA 2562

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2202 TATATAASEEPAPEHGhKPAHQASETELAA----AIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGLHEAESGIL 2277
Cdd:PHA03247 2563 APDRSVPPPRPAPRPS-EPAVTSRARRPDAppqsARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPH 2641

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2278 ETGTATESSAPQVSAL--------------DPPEGSADTKETR--------GNSGDSVQ-EAKGSKVEVTPPRKDKGRQK 2334
Cdd:PHA03247 2642 PPPTVPPPERPRDDPApgrvsrprrarrlgRAAQASSPPQRPRrraarptvGSLTSLADpPPPPPTPEPAPHALVSATPL 2721

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2335 TTRRRKRNANKKVVAITETRASEAEQTQSESPAAEEATAATPEAPQEEKQSEKPPSPPAECTFDPSKTPPAESLSQENSA 2414
Cdd:PHA03247 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2415 AEKTPCKAPVL---PALPPLSQPALMDDGPQArfkvhsiieSDPVTPPSDSGIPPPTIPLVTiAKLPPPVIPGGVPHQSP 2491
Cdd:PHA03247 2802 WDPADPPAAVLapaAALPPAASPAGPLPPPTS---------AQPTAPPPPPGPPPPSLPLGG-SVAPGGDVRRRPPSRSP 2871

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2492 PPKVTEwitrQEEPRAQSTPSPALPPDTKAsdmdtssstlrkiLMDPKYVSATGVTSTSVTSAIAEPVSAPCLQEAPAPP 2571
Cdd:PHA03247 2872 AAKPAA----PARPPVRRLARPAVSRSTES-------------FALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP 2934

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674 2572 CDPKHPPlegvsaAAVPNADTQASEVPVAADKEKVAPVIAPkitsviSRMPVSIDLENSQKITLAKPAPQT 2642
Cdd:PHA03247 2935 PPPRPQP------PLAPTTDPAGAGEPSGAVPQPWLGALVP------GRVAVPRFRVPQPAPSREAPASST 2993
RRM1_RBM15B cd12554
RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from ...
 341-410 3.70e-05

RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subfamily corresponds to the RRM1 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409970 [Multi-domain]  Cd Length: 80  Bit Score: 44.42  E-value: 3.70e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  341 VQNLPVRSTDTSLKDGLFHEFKKFGKVTSVQIHGASEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:cd12554     7 VSNLGSQLPDELLEDGLFHEFKKFGEVSVKLSHTPELGRVAYVNFRHPEDAKEARHAKGRLVLYDRPLKV 76
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
 526-586 3.77e-05

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 44.14  E-value: 3.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  526 LSSNVSDQYLTRHFCRYGPVV--KVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12362     6 LPNEFTDQDLYQLFAPFGNVVsaKVFVDKNtgrsKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
 8-62 3.96e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 44.44  E-value: 3.96e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKR--GSEGGVaAFVDFVDIKSAQKA 62
Cdd:cd12579     2 LFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKdtGKKRGF-GFVYFEDHDSADKA 57
RRM_U2AF35_like cd12287
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
 523-590 4.21e-05

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409729 [Multi-domain]  Cd Length: 101  Bit Score: 44.95  E-value: 4.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  523 LDGLSSNVSDQYLTRHF-----------CRYGPVVKVVF-----DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12287    18 LDDGSLTLSEEEIQEHFdefyedvflelSRFGEIEDLVVcsnlnDHLLGNVYVKFESEEDAEAALQALNGRYYAGRPLYP 97


                  ....
gi 568931674  587 DFAN 590
Cdd:cd12287    98 ELSP 101
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 441-514 4.36e-05

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 43.97  E-value: 4.36e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  441 TLFIGNL-EKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12233     1 TLFVVGFdPGTTREEDIEKLFEPFGPLVRCDIRK-----TFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
PRK14949 PRK14949
DNA polymerase III subunits gamma and tau; Provisional
 1619-1789 4.49e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237863 [Multi-domain]  Cd Length: 944  Bit Score: 49.72  E-value: 4.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1619 KPKE-AEKQEEPETHPKTPePAAETKEPEPKAPVSagLPAVTVTVVTPEPAssapekaeeaaeapspagEKPAEPAPVSE 1697
Cdd:PRK14949  630 SPKEgDGKKSSADRKPKTP-PSRAPPASLSKPASS--PDASQTSASFDLDP------------------DFELATHQSVP 688

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1698 ETKLVSEPASVPVEQPRQSDVPPGEDsrdsQDSAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQV---ESSVDPKPSS 1774
Cdd:PRK14949  689 EAALASGSAPAPPPVPDPYDRPPWEE----APEVASANDGPNNAAEGNLSESVEDASNSELQAVEQQathQPQVQAEAQS 764

                         170
                  ....*....|....*
gi 568931674 1775 PQPLSKLTQRSEEAE 1789
Cdd:PRK14949  765 PASTTALTQTSSEVQ 779
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
 517-591 4.54e-05

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 44.14  E-value: 4.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  517 PTNCVWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFDRL---KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 591
Cdd:cd12412     1 IPNRIFVGGIDWDTTEEELREFFSKFGKVkdVKIIKDRAgvsKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNVGPAIR 80
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
 521-586 4.69e-05

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 44.11  E-value: 4.69e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPV--VKVVFD---RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12418     3 VRVSNLHPDVTEEDLRELFGRVGPVksVKINYDrsgRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKV 73
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
 441-510 5.79e-05

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 43.58  E-value: 5.79e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12599     1 RVYVGNLPMDIREREVEDLFSKYGPVVSIDLKIPPRPPAYAFVEFEDARDAEDAIRGRDGYDFDGHRLRV 70
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
 442-509 6.23e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 43.77  E-value: 6.23e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvnGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12373     2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVAR--NPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVR 67
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1581-1858 6.73e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.01  E-value: 6.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1581 ASEGANSTSDSVQEPVVlfhsrfMELTRMQQKEKEKDQKPKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTV 1660
Cdd:PHA03307   57 AGAAACDRFEPPTGPPP------GPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSP 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1661 TVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEETKLVSEPASVPvEQPRQSDVPPGEDSRDSQDSAALAPSAPQE 1740
Cdd:PHA03307  131 APDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSP-EETARAPSSPPAEPPPSTPPAAASPRPPRR 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1741 SaATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQPLSKLTQRSE----------------EAEEGKVEKPDTTPSTEP 1804
Cdd:PHA03307  210 S-SPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENEcplprpapitlptriwEASGWNGPSSRPGPASSS 288

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568931674 1805 DATqnagvaSEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKP 1858
Cdd:PHA03307  289 SSP------RERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESS 336
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 8-77 6.77e-05

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 43.55  E-value: 6.77e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIL--PKRGSEGGVaAFVDFVDIKSAQKAHNSVN--KMGDRDLRTD 77
Cdd:cd12448     1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPtdRETGQPKGF-GYVDFSTIDSAEAAIDALGgeYIDGRPIRLD 73
SPOC_FPA-like cd21546
SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering ...
 3488-3632 7.61e-05

SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering time control protein FPA and similar proteins; FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. FPA cotranscriptionally recognizes aberrant RNA and marks it for silencing. It controls alternative cleavage and polyadenylation on pre-mRNAs and antisense RNAs. FPA functions redundantly with FCA to prevent the expression of distally polyadenylated antisense RNAs at the FLC locus. FPA belongs to the Spen (split end) protein family, whose members contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439209  Cd Length: 125  Bit Score: 44.98  E-value: 7.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3488 VWQGLLAlKNDT--AAVQLHFVSGNNVLAHRSLPlseggPPLRIAQRMRLEASQLEGVARRMtvetdyCLLLALPCGRDQ 3565
Cdd:cd21546     1 KWSGTLA-KSGKprCNVVAHPVSGDVAREPVSLP-----EVLNVSHRTDLEEVAHKPVARAV------LVLLFAPENESD 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3566 EDVVSQteslkaaFITYLQAKQAAGIINVPnpgsnqPAYVLQIFPPCEFSESHLSRLAPD---LLASISN 3632
Cdd:cd21546    69 RGAFDE-------FIDYLSSKDRAGVVKLP------DNRTLYLVPPSEELFSQLLLNVIRqncLLGIVLP 125
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 8-68 7.70e-05

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 43.49  E-value: 7.70e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKI----LPKRgSEGgvAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12316     2 LFVRNLPFTATEDELRELFEAFGKISEVHIpldkQTKR-SKG--FAFVLFVIPEDAVKAYQELDG 63
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 526-589 7.77e-05

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 43.55  E-value: 7.77e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFDRLKG--MALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12352     6 LDRQVTEDLILQLFSQIGPCksCKMITEHGGNdpYCFVEFYEHNHAAAALQAMNGRKILGKEVKVNWA 73
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 533-589 8.04e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 43.62  E-value: 8.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  533 QYLTRHFCRYGPVVKVVFDR-----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12675    16 VHLKKLFGRYGKVVEATIPRkkggkLSGFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWA 77
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
 440-500 8.20e-05

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 44.61  E-value: 8.20e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDG 500
Cdd:cd21615    19 KTLFVGRLDYSLTELELQKKFSKFGEIEKIRIvrdKETGKSRGYAFIVFKSESDAKNAFKEGNG 82
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
 510-593 8.51e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 45.41  E-value: 8.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  510 LGFGKSMPTNcVWLDGLSSNVSDQYLTRHFCRYGPVV--KVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNK 583
Cdd:PLN03134   27 LGSLRLMSTK-LFIGGLSWGTDDASLRDAFAHFGDVVdaKVIVDRetgrSRGFGFVNFNDEGAATAAISEMDGKELNGRH 105

                          90
                  ....*....|
gi 568931674  584 IKVDFANRES 593
Cdd:PLN03134  106 IRVNPANDRP 115
RRM3_RBM15 cd12557
RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
 521-590 9.01e-05

RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409973 [Multi-domain]  Cd Length: 73  Bit Score: 43.39  E-value: 9.01e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGG--NKIKVDFAN 590
Cdd:cd12557     2 LWVGGLGPWVPLAALAREFDRFGTIRTIDYRKGDSWAYIQYESLDAAQAACTHMRGFPLGGpdRRLRVDFAD 73
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 8-68 9.06e-05

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 43.00  E-value: 9.06e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKrgseggvAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12251     4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD-------YAFVHFEERDDAVKAMEEMNG 57
RRM4_MRN1 cd12522
RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This ...
 5-78 9.24e-05

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409942 [Multi-domain]  Cd Length: 81  Bit Score: 43.67  E-value: 9.24e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    5 TRHLWVGNL--PENVREEKIIEHFKRYGRVESVKILPKRGseggvAAFVDFVDIKSAQKAHNSV-NKMGDRDLRTDY 78
Cdd:cd12522     3 SRNVYIGNIddVRVLTEERLRHDFSQYGEIEQVNFLREKN-----CAFVNFTNIANAIKAIDKIkSKPYYKDLKINF 74
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 440-510 9.38e-05

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 43.36  E-value: 9.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEI--VDIDIKKVNGVPQ-YAFLQYCDIASVCKAIK------KMDGEYLGNNRLKL 510
Cdd:cd12415     1 KTVFIRNLSFDTTEEDLKEFFSKFGEVkyARIVLDKDTGHSKgTAFVQFKTKESADKCIEaandesEDGGLVLDGRKLIV 80
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 8-67 1.01e-04

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 43.16  E-value: 1.01e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSeggvaAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12340     2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDSNF-----AFVEFEELEDAIRAKDSVH 56
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1636-1862 1.04e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 48.31  E-value: 1.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1636 PEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVS---EETKLVSEPASVPVEQ 1712
Cdd:PRK07003  374 ARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPAtadRGDDAADGDAPVPAKA 453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1713 PRQSDVPPGEDSRDSQDSAALAPSApqeSAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPqplsKLTQRSEEAEEGK 1792
Cdd:PRK07003  454 NARASADSRCDERDAQPPADSGSAS---APASDAPPDAAFEPAPRAAAPSAATPAAVPDARAP----AAASREDAPAAAA 526

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674 1793 VEKPDTTPStEPDATQNAGVASEAQppASEDVEANPPV-AAKDRKTNKSKRSKtsvQAAAASVVEKPVTRK 1862
Cdd:PRK07003  527 PPAPEARPP-TPAAAAPAARAGGAA--AALDVLRNAGMrVSSDRGARAAAAAK---PAAAPAAAPKPAAPR 591
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 442-510 1.09e-04

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 43.17  E-value: 1.09e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12448     1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLptdRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
 441-510 1.13e-04

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 42.88  E-value: 1.13e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVdiDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12529     3 TLVVFNLDPSISNDDLHQIFGAYGEIK--EIRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRIKL 70
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
 440-515 1.16e-04

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 43.22  E-value: 1.16e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKmDGEYLGNNRLKLGFGKS 515
Cdd:cd12225     1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTRFAWVEFATDASALSALNL-DGTTLGGHPLRVSPSKT 75
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 441-510 1.19e-04

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 42.63  E-value: 1.19e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDI--DIKKVNgvpQYaFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12276     3 TLLVFNLDAPVSNDELKSLFSKFGEIKEIrpTPDKPS---QK-FVEFYDVRDAEAALDGLNGRELLGGKLKV 70
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 5-62 1.25e-04

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 42.78  E-value: 1.25e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12350     2 TRTLFIGNLEKTTTYGDLRNIFERFGEIIDIDI--KKQNGNPQYAFLQYCDIASVVKA 57
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 440-500 1.26e-04

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 43.38  E-value: 1.26e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDG 500
Cdd:cd12236     2 KTLFVARLSYDTTESKLRREFEKYGPIKRVRLvrDKKTGKSRgYAFIEFEHERDMKAAYKHADG 65
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
 5-78 1.29e-04

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 42.75  E-value: 1.29e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGseggvAAFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12351     7 TNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKG-----MALVLYDEVECAQAAVKETKgrKIGGRKIQVDF 77
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 521-587 1.31e-04

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 42.78  E-value: 1.31e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVF------DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVD 587
Cdd:cd12448     1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLptdretGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRLD 73
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
 439-508 1.32e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 42.90  E-value: 1.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKV------NGVpQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd21619     1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVRRPPIhtdkadRTT-GFGFIKYTDAESAERAMQQADGILLGRRRL 75
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
 442-500 1.34e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 42.51  E-value: 1.34e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIK----KMDG 500
Cdd:cd12325     1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKdpATGRSRgFGFVTFKDPSSVDAVLAarphTLDG 66
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
 442-508 1.41e-04

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 42.53  E-value: 1.41e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIkkvngVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12609     3 IFVGNVSATCTSDELRGLFEEFGRVVECDK-----VKDYAFVHMEREEEALAAIEALNGKEVKGRRI 64
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 8-69 1.49e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 42.61  E-value: 1.49e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILpkRGSEGGVA---AFVDFVDIKSAQKAHNSVNKM 69
Cdd:cd12361     2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQIL--RDKQTGQSkgcAFVTFSTREEALRAIEALHNK 64
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 339-409 1.52e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 42.61  E-value: 1.52e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674   339 IKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQI----HGASeERYGLVFFRQQEDQEKALTASKGKLFFGMQIE 409
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKD----LFSKFGPIKSIRLvrdeTGRS-KGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM1_hnRNPD_like cd12575
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
 442-501 1.60e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409989 [Multi-domain]  Cd Length: 72  Bit Score: 42.55  E-value: 1.60e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIK----KMDGE 501
Cdd:cd12575     1 MFIGGLSWDTSKKDLKDYFSKFGEVVDCTIKldPVTGRSRgFGFVLFKDAESVDKVLDqkehKLDGK 67
RRM2_TDP43 cd12322
RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
 6-61 1.63e-04

RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409761 [Multi-domain]  Cd Length: 71  Bit Score: 42.31  E-value: 1.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKIlPK--RGseggvAAFVDFVDIKSAQK 61
Cdd:cd12322     1 RKVFVGRCTEDMTEDDLRQYFSQFGEVTDVFI-PKpfRA-----FAFVTFADDEVAQS 52
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 6-71 1.69e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 42.59  E-value: 1.69e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKIL--PKRGSEGGVaAFVDFVDIKSAQK---AHNSVNKMGD 71
Cdd:cd12415     1 KTVFIRNLSFDTTEEDLKEFFSKFGEVKYARIVldKDTGHSKGT-AFVQFKTKESADKcieAANDESEDGG 70
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 7-68 1.71e-04

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 42.63  E-value: 1.71e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILP-KRGSEGGVAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12417     1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTsARTPGSRCYGYVTMASVEEADLCIKSLNK 63
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
 442-485 1.84e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 42.56  E-value: 1.84e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ--YAFLQY 485
Cdd:cd12226     2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDrgFAYIDL 47
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
 10-62 1.99e-04

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 42.16  E-value: 1.99e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568931674   10 VGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEG--GVaAFVDFVDIKSAQKA 62
Cdd:cd12365     3 VGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDREPNLprGY-AYVEFESPEDAEKA 56
PTZ00121 PTZ00121
MAEBL; Provisional
 1687-2192 2.05e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.44  E-value: 2.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1687 EKPAEPAPVSEETKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPcvNAEPLTPGTTVSQVES 1766
Cdd:PTZ00121 1223 AKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELK--KAEEKKKADEAKKAEE 1300

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1767 --SVDPKPSSPQPLSKLTQRSEEAEEGKvEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVA-AKDRKTNKSKRS 1843
Cdd:PTZ00121 1301 kkKADEAKKKAEEAKKADEAKKKAEEAK-KKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAeAAEKKKEEAKKK 1379

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1844 KTSVQAAAASVVEKPVTRKSERIDREKLKRSSSPRGEAQKLLELKMEAEKITRTASKSSGGDTEHPEPSLPLSRSRRRNV 1923
Cdd:PTZ00121 1380 ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKA 1459

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1924 RSVYATMTDHESRSPAKEPVEQPRvTRKRLERELQEAvvppttprRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWRSP 2003
Cdd:PTZ00121 1460 EEAKKKAEEAKKADEAKKKAEEAK-KADEAKKKAEEA--------KKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKA 1530

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2004 RSQKSAAAAgpqgkrgRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDR--RDPSTDKNGPDTFPVEVLERKPP 2081
Cdd:PTZ00121 1531 EEAKKADEA-------KKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMalRKAEEAKKAEEARIEEVMKLYEE 1603

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2082 EKTYKSKrgRARSTRSAMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLANNPADPDREAEEES 2161
Cdd:PTZ00121 1604 EKKMKAE--EAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAK 1681

                         490       500       510
                  ....*....|....*....|....*....|.
gi 568931674 2162 ASASTAPPEGTQLARQIELEQAVQNIAKLPE 2192
Cdd:PTZ00121 1682 KAEEDEKKAAEALKKEAEEAKKAEELKKKEA 1712
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
 442-510 2.12e-04

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 42.65  E-value: 2.12e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12383     9 IFCGDLGNEVTDEVLARAFSKYPSFQKAKVirdKRTGKSKGYGFVSFKDPNDYLKALREMNGKYVGNRPIKL 80
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 442-500 2.16e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 42.33  E-value: 2.16e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGVpqyAFLQYCDIASVCKAIKKMDG 500
Cdd:cd12316     2 LFVRNLPFTATEDELRELFEAFGKISEVHIpldkqtKRSKGF---AFVLFVIPEDAVKAYQELDG 63
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1549-1963 2.20e-04

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 47.38  E-value: 2.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1549 SSIFEQDSKRLQHLERKSEEPDLPPGGLYGRQASEGA---NSTSDSVQEPVVLFHSRFMELTR--------------MQQ 1611
Cdd:PTZ00449  497 APIEEEDSDKHDEPPEGPEASGLPPKAPGDKEGEEGEhedSKESDEPKEGGKPGETKEGEVGKkpgpakehkpskipTLS 576

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1612 KEKEKDQKPKEAEKQEEPEThPKTP-EPAAETKEPEPKAPVSAGLPAvtvtvvTPEPASSAPEKAEEAAEAPSPAGEKPA 1690
Cdd:PTZ00449  577 KKPEFPKDPKHPKDPEEPKK-PKRPrSAQRPTRPKSPKLPELLDIPK------SPKRPESPKSPKRPPPPQRPSSPERPE 649

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1691 EP-APVSEETKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPCVNAEPLT---------PGTT 1760
Cdd:PTZ00449  650 GPkIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTtprplppklPRDE 729

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1761 VSQVESSVDPKPSSPQPLSKLTQRSEEAEEGKvEKPDTTPST--------EPDATQNAGVASEA--QPPASEDVEANPP- 1829
Cdd:PTZ00449  730 EFPFEPIGDPDAEQPDDIEFFTPPEEERTFFH-ETPADTPLPdilaeefkEEDIHAETGEPDEAmkRPDSPSEHEDKPPg 808

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1830 ----VAAKDRKTNKSKRSKTSVQAAAASVVEKPVTRKSeridreKLKRSSSPRGEAQKLLELKMEAEkITRTASKSSG-- 1903
Cdd:PTZ00449  809 dhpsLPKKRHRLDGLALSTTDLESDAGRIAKDASGKIV------KLKRSKSFDDLTTVEEAEEMGAE-ARKIVVDDDGte 881

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1904 GDTEHPEPSlplsrsrrrnvrsVYATMTDHESRSPAKEPVEQPRVTRKRLERELQEAVVP 1963
Cdd:PTZ00449  882 ADDEDTHPP-------------EEKHKSEVRRRRPPKKPSKPKKPSKPKKPKKPDSAFIP 928
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 442-502 2.30e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 42.22  E-value: 2.30e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEY 502
Cdd:cd12361     2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQIlrDKQTGQSKgCAFVTFSTREEALRAIEALHNKK 65
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 441-516 2.39e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 42.14  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  441 TLFIGNLEKTTTYHDLRN----IFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLgnnrlklgFGKSM 516
Cdd:cd12246     1 TLYINNLNEKIKKDELKRslyaLFSQFGPVLDIVASKSLKMRGQAFVVFKDVESATNALRALQGFPF--------YGKPM 72
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
 526-589 2.39e-04

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 42.41  E-value: 2.39e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd21609     7 IPRNVTSEELAKIFEEAGTVeiAEVMYDRYtgrsRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNIT 76
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 341-411 2.42e-04

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 41.85  E-value: 2.42e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  341 VQNLPVRSTDTSLKDglfhEFKKFGKVTSVQIhgasEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12251     6 VRNLMLSTTEEKLRE----LFSEYGKVERVKK----IKDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVS 68
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
 6-62 2.51e-04

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 41.90  E-value: 2.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12336     2 RTLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKNFAFVTFKHEVSVPYA 58
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 5-67 2.66e-04

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 42.18  E-value: 2.66e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    5 TRHLWVGN--LPENVREEKIIEHFKRYGRVESVKILPkrgseGGVAAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12431     1 TQHLVVANggLGNGVSREQLLEVFEKYGTVEDIVMLP-----GKPYSFVSFKSVEEAAKAYNALN 60
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
 442-512 2.79e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 241042 [Multi-domain]  Cd Length: 72  Bit Score: 41.71  E-value: 2.79e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12598     2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVEF 72
RRM2_Crp79_Mug28 cd21621
RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
 339-411 3.14e-04

RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410200 [Multi-domain]  Cd Length: 74  Bit Score: 41.54  E-value: 3.14e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  339 IKVQNLPvrsTDTSLKDgLFHEFKKFGKVTSVQIHGA---SEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd21621     1 LTVLNLP---TDMTPKD-LYNLFSEHGKVEGTAINQVpdnRGRRYGEVAMNSYEDCQKALEYFNGYVYKGYILEVF 72
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
 8-68 3.48e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 41.79  E-value: 3.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDF-VDIKSAQKAHNSVNK 68
Cdd:cd12226     2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDRGFAYIDLrTSEAALQKCLSTLNG 63
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
 8-62 3.52e-04

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 41.66  E-value: 3.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12599     2 VYVGNLPMDIREREVEDLFSKYGPVVSIDL--KIPPRPPAYAFVEFEDARDAEDA 54
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 440-512 3.66e-04

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 41.73  E-value: 3.66e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12398     1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVtdRETGKPKgYGFCEFRDAETALSAVRNLNGYELNGRPLRVDF 76
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
 5-68 3.87e-04

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 41.49  E-value: 3.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESV-KILPKRGseggvAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12524     1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLyTACKHRG-----FIMVSYYDIRAAQSAKRALQG 60
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1806-2215 3.94e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 46.70  E-value: 3.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1806 ATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSV----QAAAASVVEKPVTRKSERIDREKLKRSSSPRGEA 1881
Cdd:PHA03307   12 EAAAEGGEFFPRPPATPGDAADDLLSGSQGQLVSDSAELAAVtvvaGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1882 QKLLELKMEAEKITRTASKSSGGDTEH-------PEPSLPLSRSRRRNVRSVYATMTDHESRSPAKEPVEQPRVTRKRLE 1954
Cdd:PHA03307   92 LSTLAPASPAREGSPTPPGPSSPDPPPptpppasPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQ 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1955 REL-----QEAVVPPTTPRRGRPPKTRRRAEEDGEHERKEPAE------TPRPAEGWRSPRSQKSAAAAGPQGKR----G 2019
Cdd:PHA03307  172 AALplsspEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISasasspAPAPGRSAADDAGASSSDSSSSESSGcgwgP 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2020 RNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRD---RRDPSTDKNGPDTFPvevlerKPPEKTYKSKRGRARSTR 2096
Cdd:PHA03307  252 ENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSsprERSPSPSPSSPGSGP------APSSPRASSSSSSSRESS 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2097 SAMDRAAHQRSlemaaraagqaaDKEAGPAAASPQESESPQKGSGSSPqlannPADPDREAEEESASASTAPPEGTQL-- 2174
Cdd:PHA03307  326 SSSTSSSSESS------------RGAAVSPGPSPSRSPSPSRPPPPAD-----PSSPRKRPRPSRAPSSPAASAGRPTrr 388

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 568931674 2175 -ARQIELEQAVQNIAKLPEPSAAAASKGTATATAASEEPAPE 2215
Cdd:PHA03307  389 rARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASGAFYARY 430
RRM2_hnRNPA3 cd12582
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) ...
 6-69 3.94e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409996 [Multi-domain]  Cd Length: 80  Bit Score: 41.86  E-value: 3.94e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDiksaqkaHNSVNKM 69
Cdd:cd12582     1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGfAFVTFDD-------HDTVDKI 58
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 526-591 4.01e-04

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 41.68  E-value: 4.01e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFD----RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANR 591
Cdd:cd12674     8 LPFDVTLESLTDFFSDIGPVkhAVVVTDpetkKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKP 79
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 9-67 4.06e-04

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 41.50  E-value: 4.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674    9 WVGNLPENVREEKIIEHFKRYGRVESVKILPKRGseggvAAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12354     4 YVGNITKGLTEALLQQTFSPFGQILEVRVFPDKG-----YAFIRFDSHEAATHAIVSVN 57
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
 8-78 4.40e-04

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 41.24  E-value: 4.40e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKR--GSEGGVAaFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12375     2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKitGQSLGYG-FVNYRDPNDARKAINTLNglDLENKRLKVSY 75
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
 441-511 4.57e-04

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 41.12  E-value: 4.57e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGV-PQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 511
Cdd:cd21603     2 AIFVKNLPLDTNNDEILDFFSKVGPIKSVFTSPKYKYnSLWAFVTYKKGSDTEKAIKLLNGTLFKGRTIEVT 73
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
 339-411 4.62e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 41.10  E-value: 4.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  339 IKVQNLPVRSTdtslKDGLFHEFKKFGKVTSVQI---HGASEER-YGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12311     1 LKVDNLTYRTT----PDDLRRVFEKYGEVGDVYIprdRYTRESRgFAFVRFYDKRDAEDAIDAMDGAELDGRELRVQ 73
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 441-500 4.80e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 41.39  E-value: 4.80e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDG 500
Cdd:cd21608     1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVItdRETGRSRgFGFVTFSTAEAAEAAIDALNG 63
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
 8-69 5.04e-04

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 40.86  E-value: 5.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPkrgsegGVAAFVdFVDIKSAQKAHNSVNKM 69
Cdd:cd21617     2 VYVGNLPLDISEEEILQLFKAFNPVLVKKIRS------GFKCFA-FVDLGSDENVKLAIQQL 56
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 10-68 5.12e-04

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 41.01  E-value: 5.12e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674   10 VGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12565     5 VKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKDGKSRRFGFIGFKSEEEAQKAVKYFNK 63
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1646-1835 5.64e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 46.00  E-value: 5.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1646 EPkAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEETKLVSEPASVPVEQPRQSDVPPGEdSR 1725
Cdd:PRK07003  359 EP-AVTGGGAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPA-TA 436

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1726 DSQDSAALAPSAPQESAATDAVPCVNAEPLTPgTTVSQVESSVDPKPSSPQPLSKltqrseEAEEGKVEKPDTTPSTEPD 1805
Cdd:PRK07003  437 DRGDDAADGDAPVPAKANARASADSRCDERDA-QPPADSGSASAPASDAPPDAAF------EPAPRAAAPSAATPAAVPD 509

                         170       180       190
                  ....*....|....*....|....*....|..
gi 568931674 1806 ATQNAGVASE--AQPPASEDVEANPPVAAKDR 1835
Cdd:PRK07003  510 ARAPAAASREdaPAAAAPPAPEARPPTPAAAA 541
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 8-68 5.69e-04

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 40.85  E-value: 5.69e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSeGGVAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12352     1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMITEHGG-NDPYCFVEFYEHNHAAAALQAMNG 60
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1618-1816 5.89e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 5.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1618 QKPKEAEKQEEPETHPKTPEPAAETKEPEPKAPvsAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSE 1697
Cdd:PRK07764  604 ASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAP--AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAP 681

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1698 ETKLVS--------EPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPcVNAEPLTPGTTVSQVESSVD 1769
Cdd:PRK07764  682 PPAPAPaapaapagAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVP-LPPEPDDPPDPAGAPAQPPP 760

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 568931674 1770 PKPSSPQPLSKLTQRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEA 1816
Cdd:PRK07764  761 PPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAEEVAME 807
Collagen_mid pfam15984
Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial ...
 2641-2719 6.49e-04

Bacterial collagen, middle region; Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.


Pssm-ID: 435053 [Multi-domain]  Cd Length: 198  Bit Score: 43.86  E-value: 6.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  2641 QTLTGLVSALTGLVNVSLVPVNALKGPVKGSVATLKGLVSTPAGPVN--LLKGPVNVLTGPVNVLTTPVSATVG----TV 2714
Cdd:pfam15984   60 NAVTSAGQLVSGLGTGPLAPLAPVTTPLGGTVSTLGGAVTGGGTTLGtaLSTGPVQQLTQQVSSAITPITSTVTgttqTV 139


                   ....*
gi 568931674  2715 NAAPG 2719
Cdd:pfam15984  140 GAATG 144
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
 438-498 6.61e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 40.88  E-value: 6.61e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVpqyAFLQYCDIASVCKAIKKM 498
Cdd:cd12523     2 ASRNVYLGNLPESITEEELREDLEKFGPIDQIKIVKEKNI---AFVHFLSIANAIKVVTTL 59
RRM1_hnRPDL cd12758
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
 442-509 6.62e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 410152 [Multi-domain]  Cd Length: 76  Bit Score: 41.12  E-value: 6.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIK----KMDGEYLGNNRLK 509
Cdd:cd12758     2 MFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTdpVTGRSRgFGFVLFKDAASVDKVLElkehKLDGKLIDPKRAK 76
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 3288-3480 6.62e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.80  E-value: 6.62e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3288 APAQQLTHTQFPVASSISLASRTKTSAQvppEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAQPPSGKIPQVS 3367
Cdd:pfam09770  170 AAAPAPAPQPAAQPASLPAPSRKMMSLE---EVEAAMRAQAKKPAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQP 246

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3368 QEAKGtqtggveqtrlPAIPTNRPSEPHAQLQRAPVETAQPAHPSPVSVSmKPDLPSPLSSQAAPKQPL-----FVPANS 3442
Cdd:pfam09770  247 QQQPQ-----------QPQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQA-QQFHQQPPPVPVQPTQILqnpnrLSAARV 314

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 568931674  3443 GPSTPPGLALPHAEVQPAPKQESSPHGTPQ---RPVDMVQL 3480
Cdd:pfam09770  315 GYPQNPQPGVQPAPAHQAHRQQGSFGRQAPiitHPQQLAQL 355
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
 529-586 7.06e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 40.69  E-value: 7.06e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  529 NVSDQYLTRHFCRYGPVVKVVFdrLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12341    12 QMTKEDLEEIFSKYGKILGISL--HKGYGFVQFDNEEDARAAVAGENGRTIKGQRLDI 67
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 539-589 7.37e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 40.60  E-value: 7.37e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568931674  539 FCRYGPVVKVVF---DRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12246    24 FSQFGPVLDIVAsksLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYA 77
RRM_FET cd12280
RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...
 521-588 7.51e-04

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.


Pssm-ID: 409722 [Multi-domain]  Cd Length: 82  Bit Score: 40.86  E-value: 7.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYG----------PVVKVVFDR----LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12280     1 IFVSGLPPDVTIDELADLFGQIGiikrykdtwpPKIKIYTDKetgkPKGEATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80


                  ..
gi 568931674  587 DF 588
Cdd:cd12280    81 SL 82
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 4-68 8.03e-04

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 40.86  E-value: 8.03e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    4 ETRHLWVGNLPENVREEKIIEHFKRYGRVESVKI-LPKRGSEGGVAAFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12566     1 ETGRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVpIDKKTKKSKGFAYVLFLDPEDAVQAYNELDG 66
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 8-81 8.86e-04

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 40.44  E-value: 8.86e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKAHNSVNKM--GDRDLRTDYNEP 81
Cdd:cd12297     3 LWVTNFPPSYDERSIRDLFGDYGVILSVRLPSLRYNTSRRFCYIDFTSPESARAAVELLNGLleEGYTLVVKISDP 78
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1642-1877 8.98e-04

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 45.30  E-value: 8.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1642 TKEPEPKAPVSAGLPA-VTVTVVTPEPASSAPEKAEEAAEAPSPageKPAEPAPVSEETKLVSEPASVP----VEQPRQS 1716
Cdd:PLN03209  325 SQRVPPKESDAADGPKpVPTKPVTPEAPSPPIEEEPPQPKAVVP---RPLSPYTAYEDLKPPTSPIPTPpsssPASSKSV 401

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1717 DVPPGEDSRDSQDSAALAPSAPQESAATdaVPCVNAEPLTPGTTVSQVESsvdpkPSSPQPLSKLTQRSEEAEEGKVEK- 1795
Cdd:PLN03209  402 DAVAKPAEPDVVPSPGSASNVPEVEPAQ--VEAKKTRPLSPYARYEDLKP-----PTSPSPTAPTGVSPSVSSTSSVPAv 474

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1796 PDTTPSTEpdATQNAGVASEAQPPASEDV---EANPPVAAKDRKTNKSKRSKTSVQAAAASVVEKPVTRKSERIDREKLK 1872
Cdd:PLN03209  475 PDTAPATA--ATDAAAPPPANMRPLSPYAvydDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKP 552


                  ....*
gi 568931674 1873 RSSSP 1877
Cdd:PLN03209  553 RPLSP 557
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
 442-510 9.02e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.


Pssm-ID: 410008 [Multi-domain]  Cd Length: 70  Bit Score: 40.31  E-value: 9.02e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKkvNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12595     2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--RG---FGFVEFEDPRDADDAVYELDGKELCNERVTI 65
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 439-500 9.12e-04

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 40.48  E-value: 9.12e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDG 500
Cdd:cd12566     2 TGRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVpidKKTKKSKGFAYVLFLDPEDAVQAYNELDG 66
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
 339-411 9.20e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 40.31  E-value: 9.20e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  339 IKVQNLPVRSTDtslKDGLFHEFKKFGKVTSVQIHGAseerYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12341     3 IFVGNLPTDQMT---KEDLEEIFSKYGKILGISLHKG----YGFVQFDNEEDARAAVAGENGRTIKGQRLDIN 68
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
 8-72 1.01e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 40.00  E-value: 1.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGseggvAAFVDFVDIKSAQKAHNSVNK---MGDR 72
Cdd:cd12337     2 VYIGRLPYRARERDVERFFRGYGRIRDINL--KNG-----FGFVEFEDPRDADDAVYELNGkelCGER 62
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 521-589 1.01e-03

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 40.50  E-value: 1.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12227     5 LWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWA 73
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 541-588 1.01e-03

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.


Pssm-ID: 409727 [Multi-domain]  Cd Length: 85  Bit Score: 40.61  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568931674  541 RYGPVVKVVFDRL--KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDF 588
Cdd:cd12285    34 KYGPVLHIYVDKNspQGNVYVKFKTIEAAQKCVQAMNGRWFDGRQITAAY 83
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 2798-3129 1.04e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 45.29  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  2798 TEGPQRISAKISQIPPASAmdiefqqsVSKSQVKADSITPTQSAPkgpqTPSAfanvaahstlvlTAQTYNASPVISSVK 2877
Cdd:pfam05109  529 TPTPNATSPTLGKTSPTSA--------VTTPTPNATSPTPAVTTP----TPNA------------TIPTLGKTSPTSAVT 584

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  2878 TDRPSLEKPepihlSVSTPVTQGGTVKVLTQGINTPPVLVHNQLVLTPSIVTTNKKLADPVTLKIEtkvLQPANLGPTLT 2957
Cdd:pfam05109  585 TPTPNATSP-----TVGETSPQANTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMS---LRPSSISETLS 656

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  2958 PHHPPALPSKLPAEVNHVPSGPS-----TPADRTIAHLATPKPdthsprptGPTPGLFPRPCHPSSTTSTALSTNATVml 3032
Cdd:pfam05109  657 PSTSDNSTSHMPLLTSAHPTGGEnitqvTPASTSTHHVSTSSP--------APRPGTTSQASGPGNSSTSTKPGEVNV-- 726

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  3033 AAGIPVPQFISSIHPE-QSVIMPPHSIT-----QTVSLGHLSQGEVRMST-PTLPSITYSIRPETLHSPRAPLQPQQIEA 3105
Cdd:pfam05109  727 TKGTPPKNATSPQAPSgQKTAVPTVTSTggkanSTTGGKHTTGHGARTSTePTTDYGGDSTTPRTRYNATTYLPPSTSSK 806

                          330       340
                   ....*....|....*....|....*..
gi 568931674  3106 RAPQRVGTPQPATTG---VPALATQHP 3129
Cdd:pfam05109  807 LRPRWTFTSPPVTTAqatVPVPPTSQP 833
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 3353-3516 1.06e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.98  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3353 SQPAQPPSGKIPQVSQEAKGTQTGGVEQTRLPAIPTNRPSEPHAQLQRAPVETAQPAHPSPVSVSMKPDLPSPLSSQAAP 3432
Cdd:PRK07764  394 PAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAA 473

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3433 KQPLFVPANSGPSTPPGLALPHAEVQPAPKQESSPHGTPQR--PvDMVQLLKQKYPIVWQGLLA----LKNDTAAVQLHF 3506
Cdd:PRK07764  474 PEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRErwP-EILAAVPKRSRKTWAILLPeatvLGVRGDTLVLGF 552

                         170
                  ....*....|
gi 568931674 3507 VSGNnvLAHR 3516
Cdd:PRK07764  553 STGG--LARR 560
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 6-62 1.08e-03

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 40.32  E-value: 1.08e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILPK----RGSEGGVAAFVDFVDIKSAQKA 62
Cdd:cd12298     1 REIRVRNLDFELDEEALRGIFEKFGEIESINIPKKqknrKGRHNNGFAFVTFEDADSAESA 61
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
 7-81 1.09e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 40.48  E-value: 1.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVN--KMGDRDLRTDYNEP 81
Cdd:cd12770     3 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGyGFVNYIDPKDAEKAINTLNglRLQTKTIKVSYARP 80
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
 7-81 1.10e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 40.48  E-value: 1.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVN--KMGDRDLRTDYNEP 81
Cdd:cd12771     6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGyGFVNYIEPKDAEKAINTLNglRLQTKTIKVSYARP 83
RRM2_hnRNPA1 cd12580
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) ...
 6-69 1.11e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.


Pssm-ID: 409994 [Multi-domain]  Cd Length: 77  Bit Score: 40.33  E-value: 1.11e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDiksaqkaHNSVNKM 69
Cdd:cd12580     1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGfAFVTFDD-------HDSVDKI 58
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
 7-62 1.13e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 40.31  E-value: 1.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGgvAAFVDFVDIKSAQKA 62
Cdd:cd12373     1 KVYVGNLGPRVTKRELEDAFEKYGPLRNVWV--ARNPPG--FAFVEFEDPRDAEDA 52
PTZ00121 PTZ00121
MAEBL; Provisional
 1602-2123 1.13e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1602 RFMELTRMQQKEKEKDQKPKEAEKQEEpetHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEA 1681
Cdd:PTZ00121 1207 KAEEERKAEEARKAEDAKKAEAVKKAE---EAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADEL 1283

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1682 PSPAGEKPAEPAPVSEETKLVSEpASVPVEQPRQSDvPPGEDSRDSQDSAALAPSAPQESAATDAVPCVNAEpltpgTTV 1761
Cdd:PTZ00121 1284 KKAEEKKKADEAKKAEEKKKADE-AKKKAEEAKKAD-EAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAE-----AAA 1356

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1762 SQVESSVDPKPSSPQPLSKLTQRSEEAEEgKVEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANppvAAKDRKTNKSK 1841
Cdd:PTZ00121 1357 DEAEAAEEKAEAAEKKKEEAKKKADAAKK-KAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKAD---EAKKKAEEKKK 1432

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1842 RSKTSVQAAAASVVEKPVTRKSERIDREKLKRSSSprgEAQKLLELKMEAEKiTRTASKSSGGDTEHPEPSLPLSRSRRR 1921
Cdd:PTZ00121 1433 ADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAE---EAKKADEAKKKAEE-AKKADEAKKKAEEAKKKADEAKKAAEA 1508

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1922 NVRSVYATMTDHesrspAKEPVEQPRVTRKRLERELQEAvvppttpRRGRPPKTRRRAEEDGEHERKEPAETPRPAEGWR 2001
Cdd:PTZ00121 1509 KKKADEAKKAEE-----AKKADEAKKAEEAKKADEAKKA-------EEKKKADELKKAEELKKAEEKKKAEEAKKAEEDK 1576

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2002 SPRSQKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTR-EGNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPVEVLeRKP 2080
Cdd:PTZ00121 1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKkAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEEL-KKA 1655

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|...
gi 568931674 2081 PEKTYKSKRGRARSTRSAMDRAAHQRSLEMAARAAGQAADKEA 2123
Cdd:PTZ00121 1656 EEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEA 1698
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
 440-510 1.15e-03

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 39.98  E-value: 1.15e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK-VNGVP-QYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12336     2 RTLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKdPNGKPkNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRI 74
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 8-65 1.15e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 40.29  E-value: 1.15e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAA----FVDFVDIKSAQKAHNS 65
Cdd:cd12318     3 LFVKNLNFKTTEEALKKHFEKCGPIRSVTIAKKKDPKGPLLSmgygFVEFKSPEAAQKALKQ 64
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
 442-515 1.16e-03

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 40.81  E-value: 1.16e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  442 LFIGNLEKTTTYH--DLRNIFQRFGEIVDIDIKKVN--GVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKS 515
Cdd:cd21622     6 LFVKNLDDTVITNkeDLEQLFSPFGQIVSSYLATYPgtGISKgFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYAER 84
RRM_Nab3p cd12342
RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) ...
 341-410 1.17e-03

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.


Pssm-ID: 240788 [Multi-domain]  Cd Length: 71  Bit Score: 40.12  E-value: 1.17e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  341 VQNLPVRSTDtslKDGLFHEFKKFGKVTSVQIHGAseerYGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:cd12342     4 IGNLPTKRVS---KEDLFRIFSPYGHLMQIVIKNA----FGFVQFDSPQSCRNAIECEQGEMNRGKKLHL 66
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
 8-62 1.17e-03

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 40.29  E-value: 1.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRG--SEGgvAAFVDFVDIKSAQKA 62
Cdd:cd12412     5 IFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAgvSKG--YGFVTFETQEDAEKI 59
RRM_G3BP1 cd12463
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 1 (G3BP1) ...
 4-83 1.19e-03

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins; This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript.


Pssm-ID: 409896 [Multi-domain]  Cd Length: 80  Bit Score: 40.24  E-value: 1.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    4 ETRHLWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGGVAAFVDFVDIKSAQKAHNSVNKMGDRDLRTDYNEPGT 83
Cdd:cd12463     2 DSHQLFVGNLPHDVDKSELKEFFQGYGNVVELRI--NSGGKLPNFGFVVFDDPEPVQKILSNRPIKFRGEVRLNVEEKKT 79
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
 338-411 1.19e-03

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 39.96  E-value: 1.19e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  338 GIKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQIHGA--SEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd21603     2 AIFVKNLPLDTNNDEILD----FFSKVGPIKSVFTSPKykYNSLWAFVTYKKGSDTEKAIKLLNGTLFKGRTIEVT 73
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
 517-589 1.23e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 40.81  E-value: 1.23e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  517 PTNCVWLDGLSSNVSDQYLTRHFCRYGPVVKVVFD------RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12559     4 PNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPldfytrRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFA 82
RRM1_CELF3_4_5_6 cd12632
RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
 442-494 1.26e-03

RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410041 [Multi-domain]  Cd Length: 87  Bit Score: 40.48  E-value: 1.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQY---AFLQYCDIASVCKA 494
Cdd:cd12632     8 LFIGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHkgcAFLTYCARESALKA 63
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 10-67 1.35e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410090 [Multi-domain]  Cd Length: 80  Bit Score: 39.95  E-value: 1.35e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674   10 VGNLPENVREEKIIEHFKRYGRVESVKILPKRGSeggvaAFVDFVDIKSaqkAHNSVN 67
Cdd:cd12689     7 VRGLSEHVTEADLVEALQNFGPISYVTMMPKKRQ-----ALVEFEDIEG---AKACVN 56
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1689-2306 1.37e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.93  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1689 PAEPAPvseeTKLVSEPASVPVeQPRQSDVPPGED---SRDSQDSAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQVE 1765
Cdd:PHA03247 2512 PSRLAP----AILPDEPVGEPV-HPRMLTWIRGLEelaSDDAGDPPPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRA 2586

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1766 SSVDPKPSSPQPlskltqRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKskrskt 1845
Cdd:PHA03247 2587 RRPDAPPQSARP------RAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRD------ 2654

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1846 svqAAAASVVEKPvtRKSERIDREKlKRSSSPRGEAQKllELKMEAEKITRTASKSSGGDTEHPEP-----SLPLSRSRR 1920
Cdd:PHA03247 2655 ---DPAPGRVSRP--RRARRLGRAA-QASSPPQRPRRR--AARPTVGSLTSLADPPPPPPTPEPAPhalvsATPLPPGPA 2726

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1921 RNVRSVYATMTDHESRSPAKEPVeQPRVTRKRLERELQEAVVPPTTPR--RGRPPKTRRRAEEDGEHERKEPAETPRPAE 1998
Cdd:PHA03247 2727 AARQASPALPAAPAPPAVPAGPA-TPGGPARPARPPTTAGPPAPAPPAapAAGPPRRLTRPAVASLSESRESLPSPWDPA 2805

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1999 GWRSPRSQKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRdRRDPStdkngpdtfpvevleR 2078
Cdd:PHA03247 2806 DPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR-RRPPS---------------R 2869

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2079 KPPEKTYKSKRGRARStrsaMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLaNNPADPDREAE 2158
Cdd:PHA03247 2870 SPAAKPAAPARPPVRR----LARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPP-PPPPRPQPPLA 2944

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2159 EESASASTAPPEGTQLARQIEL-----EQAVQNIAKLPEPSAAAASKGT--------------ATATAASEE--PAPEHG 2217
Cdd:PHA03247 2945 PTTDPAGAGEPSGAVPQPWLGAlvpgrVAVPRFRVPQPAPSREAPASSTppltghslsrvsswASSLALHEEtdPPPVSL 3024

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2218 HKPAHQASETELAAAIGSIISDAsgEPENFSAPPSVPPgsqthprEGMEPGLHEAESGILETGTATESSapqvSALDPPE 2297
Cdd:PHA03247 3025 KQTLWPPDDTEDSDADSLFDSDS--ERSDLEALDPLPP-------EPHDPFAHEPDPATPEAGARESPS----SQFGPPP 3091


                  ....*....
gi 568931674 2298 GSADTKETR 2306
Cdd:PHA03247 3092 LSANAALSR 3100
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
 10-70 1.43e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 39.80  E-value: 1.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674   10 VGNLPENVREEKIIEHFKRYGRVesVKILPKRGSEGGVA---AFVDFVDIKSAQKAHNSVNKMG 70
Cdd:cd12408     4 VTNLSEDATEEDLRELFRPFGPI--SRVYLAKDKETGQSkgfAFVTFETREDAERAIEKLNGFG 65
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
 8-78 1.49e-03

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 39.73  E-value: 1.49e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12447     2 LFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRGSGRSKGyGYVDFATPEAAQKALAAMSgkEIDGRQINVDF 75
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
 526-589 1.49e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 39.97  E-value: 1.49e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  526 LSSNVSDQYLTRHFCRYGPVVKVvfDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12495     9 LANTVTEEILEKAFSQFGKLERV--KKLKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFA 70
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 441-504 1.56e-03

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 40.08  E-value: 1.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLG 504
Cdd:cd12450     1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIamdRDDGRSKGFGHVEFASAESAQKALEKSGQDLGG 67
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
 440-514 1.58e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 39.59  E-value: 1.58e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIvdidiKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12495     2 KVLFVRNLANTVTEEILEKAFSQFGKL-----ERVKKLKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAK 71
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1616-1844 1.64e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 44.15  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1616 KDQKPKEAEKQEEPE------THPKTPEPAAETKEPEPKAPVSAGLPAVTVTV-----VTPEPASSAPEKAEEAAEAPSP 1684
Cdd:PLN03209  326 QRVPPKESDAADGPKpvptkpVTPEAPSPPIEEEPPQPKAVVPRPLSPYTAYEdlkppTSPIPTPPSSSPASSKSVDAVA 405

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1685 AGEKPaEPAPVSEETKLVSEPASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPcvNAEPLTPGT-TVSQ 1763
Cdd:PLN03209  406 KPAEP-DVVPSPGSASNVPEVEPAQVEAKKTRPLSPYARYEDLKPPTSPSPTAPTGVSPSVSST--SSVPAVPDTaPATA 482

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1764 VESSVDPKPSSPQPLSKLTQRSEeaeegkvEKPDTTPSTepdATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRS 1843
Cdd:PLN03209  483 ATDAAAPPPANMRPLSPYAVYDD-------LKPPTSPSP---AAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKP 552


                  .
gi 568931674 1844 K 1844
Cdd:PLN03209  553 R 553
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 442-519 1.71e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 39.68  E-value: 1.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK---VNGVPQYAFLQYCDIASVCKAIKKMDGEYLGnnrlklgfGKSMPT 518
Cdd:cd12353     2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKdtqTGKSKGYGFVSFVKKEDAENAIQGMNGQWLG--------GRNIRT 73


                  .
gi 568931674  519 N 519
Cdd:cd12353    74 N 74
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 442-512 1.73e-03

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 39.81  E-value: 1.73e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLpmDRETKRPRgFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNE 74
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
 341-411 1.75e-03

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 39.57  E-value: 1.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  341 VQNLPVRSTDTSLkdglfHE-FKKFGKVTSVQI--HGASEERYGLVF--FRQQEDQEKALTASKGKLFFGMQIEVT 411
Cdd:cd12393     6 VSNLPFSLTNNDL-----HQiFSKYGKVVKVTIlkDKETRKSKGVAFvlFLDRESAHNAVRAMNNKELFGRTLKCS 76
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
 442-509 1.78e-03

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 39.88  E-value: 1.78e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12411    12 IYIGGLPYELTEGDILCVFSQYGEIVDINLvrDKKTGKSKgFAFLAYEDQRSTILAVDNLNGIKLLGRTIR 82
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1621-2012 1.90e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 1.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1621 KEAEKQEEPETHPkTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEETK 1700
Cdd:PHA03307   59 AAACDRFEPPTGP-PPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEM 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1701 LVSEPASVPVeqPRQSDVPPGEDSRDSqdsAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQPLSK 1780
Cdd:PHA03307  138 LRPVGSPGPP--PAASPPAAGASPAAV---ASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSP 212

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1781 LTQRSeeaeegkvekPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAASVVE--KP 1858
Cdd:PHA03307  213 ISASA----------SSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPssRP 282

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1859 VTRKSERIDREKLKRSSSPRGEAqkllelkmEAEKITRTASKSSGGDTEHPEPSlPLSRSRRRNVRSVYATMTDHESRSP 1938
Cdd:PHA03307  283 GPASSSSSPRERSPSPSPSSPGS--------GPAPSSPRASSSSSSSRESSSSS-TSSSSESSRGAAVSPGPSPSRSPSP 353

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674 1939 AK-EPVEQPRVTRKRlerelQEAVVPPTTPRRGRPPKTRRRAEEDgEHERKEPAETPRPAEGWRSPRSQKSAAAA 2012
Cdd:PHA03307  354 SRpPPPADPSSPRKR-----PRPSRAPSSPAASAGRPTRRRARAA-VAGRARRRDATGRFPAGRPRPSPLDAGAA 422
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1963-2585 1.93e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.54  E-value: 1.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1963 PPTTPRRGRPPKTRRRAeedgeherKEPAETPRPAE---GWRSPRSQKSAAAAGPQGKRGRNEQKVEAAAEAGAQASTRE 2039
Cdd:PHA03247 2552 PPPLPPAAPPAAPDRSV--------PPPRPAPRPSEpavTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHA 2623

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2040 GNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPVEVLERKPPEKTYKSKRGRARSTRSAMDRAAHQR---SLEMAARAAG 2116
Cdd:PHA03247 2624 PDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPtvgSLTSLADPPP 2703

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2117 QAADKEAGPAAASPQE--SESPQKGSGSSPQLANNPADPdreaeeesasastAPPEGtqlarqieleqavqniaklPEPS 2194
Cdd:PHA03247 2704 PPPTPEPAPHALVSATplPPGPAAARQASPALPAAPAPP-------------AVPAG-------------------PATP 2751

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2195 AAAASKGTATATAASEEPAPEHGHKPAHQASETELAAAIGSIISDASGEPENFSAPPSVPPGSQTHPREGMEPGlheaes 2274
Cdd:PHA03247 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPA------ 2825

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2275 gileTGTATESSAPQVSALDPPEGSADTKETRGNSgdsvqeAKGSKVEVTPPRKdkgrqkttrrrkrNANKKVVAITETR 2354
Cdd:PHA03247 2826 ----GPLPPPTSAQPTAPPPPPGPPPPSLPLGGSV------APGGDVRRRPPSR-------------SPAAKPAAPARPP 2882

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2355 ASEAEQTQsespaaeeataatpEAPQEEKQSEKPPSPPaectfdPSKTPPAESLSQENSAAEKTPCKAPvlpalpPLSQP 2434
Cdd:PHA03247 2883 VRRLARPA--------------VSRSTESFALPPDQPE------RPPQPQAPPPPQPQPQPPPPPQPQP------PPPPP 2936

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2435 ALMDDGPQARFKVHSIIESDPVTPPSDSGIPPPTIPLVTIAKLPPPVIPGGVPHQSPPPKvtewiTRQEEPRAQS-TPSP 2513
Cdd:PHA03247 2937 PRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPL-----TGHSLSRVSSwASSL 3011

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674 2514 ALPPDTkasdmDTSSSTLRKILMDPKyvSATGVTSTSVTSAIAEPVSAPCLQEAPAPPCDP-KHPPLEGVSAA 2585
Cdd:PHA03247 3012 ALHEET-----DPPPVSLKQTLWPPD--DTEDSDADSLFDSDSERSDLEALDPLPPEPHDPfAHEPDPATPEA 3077
RRM_DNAJC17 cd12429
RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD ...
 531-576 1.94e-03

RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding.


Pssm-ID: 409863 [Multi-domain]  Cd Length: 74  Bit Score: 39.56  E-value: 1.94e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568931674  531 SDQYLTRHFCRYGPVVKVVF-DRLKGMALVLYSEIEDAQAAVKETKG 576
Cdd:cd12429    17 SEEELRKIFSKYGPVSDVVIsSKKKGSAIVEFATVVAADAAVENEVG 63
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
 440-510 1.97e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 39.80  E-value: 1.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KK-----VNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd21620     2 RSLYVGNLPQTCQSEDLIILFEPYGNVCGAHIasrKKvkvswVKPSKLFAFVEFETKEAATTAIVLLNGITYMGCQLKV 80
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
 526-586 1.98e-03

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 39.57  E-value: 1.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFDRL----KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12383    14 LGNEVTDEVLARAFSKYPSFqkAKVIRDKRtgksKGYGFVSFKDPNDYLKALREMNGKYVGNRPIKL 80
RRM2_TatSF1_like cd12282
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
 353-415 1.98e-03

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.


Pssm-ID: 409724 [Multi-domain]  Cd Length: 91  Bit Score: 39.91  E-value: 1.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  353 LKDGLFHEFKKFGKVTSVQIHGASEERYGLVFFRQQEDQEKALTASKGKLFFGMQIEVTAWVG 415
Cdd:cd12282    25 IKEDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKLEAETWDG 87
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 8-74 2.01e-03

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 39.46  E-value: 2.01e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIL--PKRGSEG-GvaaFVDFVDIKSAQKAhnsVNKMGDRDL 74
Cdd:cd12380     4 VYVKNFGEDVDDDELKELFEKYGKITSAKVMkdDSGKSKGfG---FVNFENHEAAQKA---VEELNGKEL 67
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
 8-67 2.09e-03

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 39.23  E-value: 2.09e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGseggvAAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12346     4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPPGKG-----CGFVQFVNRASAEAAIQKLQ 58
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
 442-507 2.19e-03

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 39.40  E-value: 2.19e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQ---YAFLQYCDIASVCKAIKK---MDGEYLGNNR 507
Cdd:cd12577     1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIMKDSATGRsrgFGFLTFEDPSSVNEVMKKehvLDGKIIDPKR 72
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 3299-3476 2.28e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.82  E-value: 2.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3299 PVASSISLASRTKTSAQVPPEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAQPPSGKIPQVSQEAKGTQTGGV 3378
Cdd:PRK07764  592 PGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPA 671

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3379 EQTrlPAIPTNRPSEPHAQLQRAPVETAQP-AHPSPVSVSMKPDLPSPLSSQAAPKQPLFVPANSGPSTPPGLALPHAEV 3457
Cdd:PRK07764  672 KAG--GAAPAAPPPAPAPAAPAAPAGAAPAqPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPP 749

                         170
                  ....*....|....*....
gi 568931674 3458 QPAPKQESSPHGTPQRPVD 3476
Cdd:PRK07764  750 DPAGAPAQPPPPPAPAPAA 768
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 525-589 2.34e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 39.47  E-value: 2.34e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  525 GLSSNVSDQYLTRHFCRYGPV--VKVVFDRL---KGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12565     7 NLPKYVTEKRLKEHFSKKGEItdVKVMRTKDgksRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
 442-518 2.43e-03

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 41.18  E-value: 2.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKSMPT 518
Cdd:PLN03134   37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVivdRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
 441-503 2.49e-03

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 39.14  E-value: 2.49e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQyAFLQYCDIASVCKAIKKMDGEYL 503
Cdd:cd12245     4 TLFVANLGPNVSEQELRQLFSRQPGFRRLRMHNKGGGPV-CFVEFEDVPFATQALNHLQGAIL 65
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2979-3480 2.54e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.16  E-value: 2.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2979 PSTPADRTIAHLATPKPDTHSPRPTGPTPglfPRPCHPSsttstalstnatvmlAAGIPVPQFISSIHPEQSVimPPHSI 3058
Cdd:PHA03247 2475 PGAPVYRRPAEARFPFAAGAAPDPGGGGP---PDPDAPP---------------APSRLAPAILPDEPVGEPV--HPRML 2534

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3059 TQTVSLGHLSQGEVRMSTPTLPSITYSIRPE-TLHSPRAPLQPQQ--IEARAPQRVGTPQPATTGVPALATQHPPEEEVH 3135
Cdd:PHA03247 2535 TWIRGLEELASDDAGDPPPPLPPAAPPAAPDrSVPPPRPAPRPSEpaVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPP 2614

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3136 YHLPVARAA--APVQSEVLVMQSEYRLHPYTVPRDVRIMVHPHVTAVSeQPRATEGVVKVPPANKAPQQLVKEAVKTSDA 3213
Cdd:PHA03247 2615 SPLPPDTHApdPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVS-RPRRARRLGRAAQASSPPQRPRRRAARPTVG 2693

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3214 KAVPAPAPVPVPVPVPTPAPPPhGEARILTVTPSSQLQGLPLT-----PPVVVTHGVQIVHSSGELFQEYRYGDVRTYHA 3288
Cdd:PHA03247 2694 SLTSLADPPPPPPTPEPAPHAL-VSATPLPPGPAAARQASPALpaapaPPAVPAGPATPGGPARPARPPTTAGPPAPAPP 2772

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3289 PAQQLTHTQFPVASSISLASRTKTSAQVPPEGEPLQSTQSAQPAPSTQATQPIPPAPPCQPSQLSQPAqPPSGKIPQVSQ 3368
Cdd:PHA03247 2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPP-PPPGPPPPSLP 2851

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 3369 EAKGTQTGGVEQTRLP-----AIPTNRPSEPHAQLQRAPVEtaqpahPSPVSVSMKPDLPSPLSSQAAPKQPLFVPANSG 3443
Cdd:PHA03247 2852 LGGSVAPGGDVRRRPPsrspaAKPAAPARPPVRRLARPAVS------RSTESFALPPDQPERPPQPQAPPPPQPQPQPPP 2925

                         490       500       510
                  ....*....|....*....|....*....|....*....
gi 568931674 3444 PS--TPPGLALPHAEVQPAPKQESSPHGTPQRPVDMVQL 3480
Cdd:PHA03247 2926 PPqpQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWL 2964
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
 518-586 2.55e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 39.43  E-value: 2.55e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  518 TNCVWLDGLSSNVSDQYLTRHFCRYGPVVKV--------VFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd21619     1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVrrppihtdKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 341-410 2.58e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 39.07  E-value: 2.58e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  341 VQNLPVRSTDTSLKDglfhEFKKFGKVTSVQI----HGASEErYGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:cd12414     4 VRNLPFKCTEDDLKK----LFSKFGKVLEVTIpkkpDGKLRG-FAFVQFTNVADAAKAIKGMNGKKIKGRPVAV 72
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
 442-502 2.62e-03

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 39.29  E-value: 2.62e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQY---AFLQYCDIASVCKAIKKMDGEY 502
Cdd:cd12637     2 LFVGSLPKTATEQEVRDLFEAYGEVEEVYLMKDPVTQQGtgcAFVKFAYKEEALAAIRSLNGTV 65
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
 440-508 2.68e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 38.77  E-value: 2.68e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  440 RTLFIGNLeKT--TTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12341     1 SRIFVGNL-PTdqMTKEDLEEIFSKYGKILGISLHK-----GYGFVQFDNEEDARAAVAGENGRTIKGQRL 65
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
 440-514 2.72e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 39.24  E-value: 2.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIvdidiKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12494     2 KVLFVRNLATTVTEEILEKTFSQFGKL-----ERVKKLKDYAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVLAK 71
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
 4-67 2.75e-03

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 39.14  E-value: 2.75e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674    4 ETRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGgvAAFVDFVDIKSAQKAHNSVN 67
Cdd:cd12241     1 VNRILYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTKETRG--TAFVVYEDIFDAKNACDHLS 62
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
 521-587 2.77e-03

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 39.06  E-value: 2.77e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVvfDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVD 587
Cdd:cd12609     3 IFVGNVSATCTSDELRGLFEEFGRVVEC--DKVKDYAFVHMEREEEALAAIEALNGKEVKGRRINVE 67
RRM_PPARGC1A_like cd12357
RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma ...
 440-485 2.78e-03

RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators; This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing.


Pssm-ID: 409793 [Multi-domain]  Cd Length: 91  Bit Score: 39.72  E-value: 2.78e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGVPQYAFLQY 485
Cdd:cd12357     3 RVVYVGKLEQDTTRSELRRRFEVFGEIEECTVHFRERGDKYGFVTY 48
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 442-508 2.78e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 39.22  E-value: 2.78e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12564     3 LIVKNLPSSITEDRLRKLFSAFGTITDVQLKytKDGKFRRFGFVGFKSEEEAQKALKHFNNSFIDTSRI 71
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 442-509 2.88e-03

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 38.93  E-value: 2.88e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI--KKVNGVPqYAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12352     1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMitEHGGNDP-YCFVEFYEHNHAAAALQAMNGRKILGKEVK 69
RRM_MCM3A_like cd12443
RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar ...
 533-579 3.03e-03

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409877 [Multi-domain]  Cd Length: 75  Bit Score: 38.84  E-value: 3.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568931674  533 QYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKetKGRKI 579
Cdd:cd12443    16 EILRRHFSKFGKVARVFCNPRKNLAIVHFKDHESAALAKK--KGKLL 60
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
 442-510 3.04e-03

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 38.95  E-value: 3.04e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEI--VDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKL 510
Cdd:cd12614     1 LYVGNLDPRVTEDLLQEIFAVTGPVenCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
 442-512 3.15e-03

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 38.75  E-value: 3.15e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAF--LQYCDIASVCKAikKMDGEYLGNNRLKLGF 512
Cdd:cd12586     4 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG---FGFirLESRTLAEIAKA--ELDGTILKSRPLRIRF 71
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
 441-498 3.37e-03

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 38.85  E-value: 3.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKM 498
Cdd:cd12290     1 TVYVELLPKNATHEWIEAVFSKYGEVVYVSIpryKSTGDPKGFAFIEFETSESAQKAVKHF 61
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1620-1777 3.38e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 43.30  E-value: 3.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1620 PKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEET 1699
Cdd:PRK07003  385 ARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCD 464

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674 1700 KLVSEPASvpveQPRQSDVPPGedsrDSQDSAALAPSAPQ-ESAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQP 1777
Cdd:PRK07003  465 ERDAQPPA----DSGSASAPAS----DAPPDAAFEPAPRAaAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPP 535
RRM2_TDP43 cd12322
RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
 440-473 3.39e-03

RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409761 [Multi-domain]  Cd Length: 71  Bit Score: 38.84  E-value: 3.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK 473
Cdd:cd12322     1 RKVFVGRCTEDMTEDDLRQYFSQFGEVTDVFIPK 34
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
 442-512 3.55e-03

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 38.82  E-value: 3.55e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12332     4 LFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGKG---FGFIRLDTRANAEAAKAELDGTPRKGRQLRVRF 71
RRM1_HuR cd12769
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup ...
 7-81 3.62e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410162 [Multi-domain]  Cd Length: 82  Bit Score: 38.86  E-value: 3.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674    7 HLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVN--KMGDRDLRTDYNEP 81
Cdd:cd12769     4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGyGFVNYVTAKDAERAINTLNglRLQSKTIKVSYARP 81
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2182-2608 3.63e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.44  E-value: 3.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2182 QAVQNIAKLPEPSAAAASKGTATATAASEEPAPEHGHKPAHQASETELAAAIGSiisDASGEPENFSAPPSVPPGSQThP 2261
Cdd:PRK07764  403 AAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSP---PPAAAPSAQPAPAPAAAPEPT-A 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2262 REGMEPGLHEAESGILETGTATESSAPQVSALDPPEGSADTKETRGNSGDSVQEAKGSKVEVTPPRKD-------KGRQK 2334
Cdd:PRK07764  479 APAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILAAVPKRSRKTWAILLPEATVLGVRGDtlvlgfsTGGLA 558

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2335 TTRRRKRNANKKVVAITE----TRASEAEQTQSESPAAEEATAATPEAPQEEKQSEkPPSPPAECTFDPSKTPPAESLSQ 2410
Cdd:PRK07764  559 RRFASPGNAEVLVTALAEelggDWQVEAVVGPAPGAAGGEGPPAPASSGPPEEAAR-PAAPAAPAAPAAPAPAGAAAAPA 637

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2411 ENSAAEKTPCKAPVLPALPPLSQPALMDDGPQARFKVHSIIESDPVTPPSDSGIPPPTIPlvtiaklpppvipggVPHQS 2490
Cdd:PRK07764  638 EASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAA---------------PAQPA 702

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2491 PPPkvtewitRQEEPRAQSTPSPALPPDTKASDMDTSSSTLRKILMDPkyvsatgvtstsvtsaiaEPVSAPCLQEAPAP 2570
Cdd:PRK07764  703 PAP-------AATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPP------------------EPDDPPDPAGAPAQ 757

                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 568931674 2571 PCDPKHPPLEGVSAAAVPNADTQASEVPVAADKEKVAP 2608
Cdd:PRK07764  758 PPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDD 795
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 525-591 3.67e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 38.71  E-value: 3.67e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  525 GLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVK--ETKGRKIGGNKIKVDFANR 591
Cdd:cd12421     6 NLPPDATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNyyTTVPPLIRGRPVYVQYSNH 74
RRM1_MSSP cd12243
RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...
 6-70 3.93e-03

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409689 [Multi-domain]  Cd Length: 71  Bit Score: 38.44  E-value: 3.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    6 RHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSE-----GgvaaFVDFVDIKSAQKAHNSVNKMG 70
Cdd:cd12243     1 TNVYIRGLPPNTTDEDLLLLCQSFGKIISTKAIIDKQTNkckgyG----FVDFDSPEAALKAIEGLNGRG 66
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 1613-1818 4.18e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 43.16  E-value: 4.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1613 EKEKDQKPKEAEKQEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVvtpEPASSAPEKAEEAAEAPSPAGEKPAEP 1692
Cdd:PRK08691  373 ENTELQSPSAQTAEKETAAKKPQPRPEAETAQTPVQTASAAAMPSEGKTA---GPVSNQENNDVPPWEDAPDEAQTAAGT 449

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1693 APVSEET-KLVSEPASVPVEQPRQSDVPPGEdsrdsqdSAALAPSAPQESAATdAVPcvNAEPLtpgttvsQVESSVDPK 1771
Cdd:PRK08691  450 AQTSAKSiQTASEAETPPENQVSKNKAADNE-------TDAPLSEVPSENPIQ-ATP--NDEAV-------ETETFAHEA 512

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 568931674 1772 PSSPQPLSKLTQRSEEAEEGKVEKPDTTPSTEPDATQNAGVASEAQP 1818
Cdd:PRK08691  513 PAEPFYGYGFPDNDCPPEDGAEIPPPDWEHAAPADTAGGGADEEAEA 559
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
 8-69 4.32e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 38.54  E-value: 4.32e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVA-AFVDFVDIKSAQKAHNSVNKM 69
Cdd:cd12650     3 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGyGFVNYVDPSDAEKAINTLNGL 65
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 521-586 4.37e-03

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 38.39  E-value: 4.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKG-MALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12276     4 LLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPsQKFVEFYDVRDAEAALDGLNGRELLGGKLKV 70
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 442-508 4.48e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 38.15  E-value: 4.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12340     2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDSN---FAFVEFEELEDAIRAKDSVHGRVLNNEPL 65
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
 441-508 4.63e-03

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 38.29  E-value: 4.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVdiDIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12527     3 SLVILNLLPAVSSFTLREIFQVYGDVK--DVRETPLKPSQRFVEFFDVRDAARALHEMNGKEIFGKRL 68
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
 526-589 4.64e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 38.54  E-value: 4.64e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  526 LSSNVSDQYLTRHFCRYGPV--VKVVFDRLKGMAL----VLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12375     7 LPQSMTQEELRSLFGAIGPIesCKLVRDKITGQSLgygfVNYRDPNDARKAINTLNGLDLENKRLKVSYA 76
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 439-512 4.66e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 38.31  E-value: 4.66e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  439 TRtLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVP-QYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGF 512
Cdd:cd12565     1 SR-IIVKNLPKYVTEKRLKEHFSKKGEITDVKVmRTKDGKSrRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEF 75
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
 441-509 4.91e-03

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 38.42  E-value: 4.91e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGVpqyAFLQYCDIASVCKAIKKMDGEYLGNNRLK 509
Cdd:cd12393     3 TVYVSNLPFSLTNNDLHQIFSKYGKVVKVTIlkdketRKSKGV---AFVLFLDRESAHNAVRAMNNKELFGRTLK 74
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1626-1835 5.05e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.94  E-value: 5.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1626 QEEPETHPKTPEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVseetklvseP 1705
Cdd:PRK12323  384 QPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPA---------P 454

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1706 ASVPVEQPRQSDVPPGEDSRDSQDSAALAPSAPQESAATDAVPCVNAEPLTPGTtvsqvessvdPKPSSPQPLSKLTQRS 1785
Cdd:PRK12323  455 AAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFAS----------PAPAQPDAAPAGWVAE 524

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 568931674 1786 EEAEEGKVEKPDTTPSTEPDATqnAGVASEAQPPASEDVEANPPVAAKDR 1835
Cdd:PRK12323  525 SIPDPATADPDDAFETLAPAPA--AAPAPRAAAATEPVVAPRPPRASASG 572
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
 524-586 5.12e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 38.40  E-value: 5.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  524 DGLSSNVSDQYLTRHFCRYGPVVKVVFDR------LKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12311     4 DNLTYRTTPDDLRRVFEKYGEVGDVYIPRdrytreSRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRV 72
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
 443-504 5.15e-03

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 38.44  E-value: 5.15e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  443 FIGNLEKTTTYHDLRNIFQRFGEIVDIDIK--KVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLG 504
Cdd:cd12306     3 YVGNVDYGTTPEELQAHFKSCGTINRVTILcdKFTGQPKgFAYIEFVDKSSVENALLLNESEFRG 67
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
 357-410 5.22e-03

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 38.18  E-value: 5.22e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  357 LFHEFKKFGKVTSVQI---HGASEER-YGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:cd12447    16 LKKEFEKYGGVISARVitdRGSGRSKgYGYVDFATPEAAQKALAAMSGKEIDGRQINV 73
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
 442-508 5.28e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410019 [Multi-domain]  Cd Length: 67  Bit Score: 38.02  E-value: 5.28e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIkkvngVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12607     3 LHVGNISSSCTNQELRAKFEEYGPVIECDI-----VKDYAFVHMERAEDAMEAIRGLDNTEFQGKRM 64
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
 440-500 5.30e-03

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 38.55  E-value: 5.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDG 500
Cdd:cd12635     2 RKLFVGMLGKQQSEDDVRRLFEPFGSIEECTIlRGPDGNSKgCAFVKFSSHAEAQAAINALHG 64
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
 442-514 5.46e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 38.07  E-value: 5.46e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKkvNGvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12337     2 VYIGRLPYRARERDVERFFRGYGRIRDINLK--NG---FGFVEFEDPRDADDAVYELNGKELCGERVIVEHAR 69
RRM_Set1B cd12549
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This ...
 13-71 5.47e-03

RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain.


Pssm-ID: 409965 [Multi-domain]  Cd Length: 93  Bit Score: 38.78  E-value: 5.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674   13 LPENVREEKIIEHFKRYGRVESVKIL--PKRGSEGGVAAFVdFVDIKSAQKA----HNSvNKMGD 71
Cdd:cd12549    10 LNDNIRENFLRDMCKKYGEVEEVEILynPKNKKHLGIAKVV-FATVKGAKDAvqhlHNT-SVMGN 72
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1619-1837 5.50e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 5.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1619 KPKEAEKQEEPETHPKT--------PEPAAETKEPEPKAPVSAGLPAVTVTVVTPEPASSAPEK---AEEAAEAPSPAGE 1687
Cdd:PHA03247 2700 DPPPPPPTPEPAPHALVsatplppgPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTagpPAPAPPAAPAAGP 2779

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1688 KPAEPAPVSEETKLVSEPASVPveqPRQSDVPPGEDSRDSQDSAALAPSAPqESAATDAVPCVNAEPLTPGTTVSQVESS 1767
Cdd:PHA03247 2780 PRRLTRPAVASLSESRESLPSP---WDPADPPAAVLAPAAALPPAASPAGP-LPPPTSAQPTAPPPPPGPPPPSLPLGGS 2855

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674 1768 VDP------KPSSPQPLSKLTQRSEEAEEgKVEKPDTTPSTEPDATQNAGVASEAQPPASEDVEANPPVAAKDRKT 1837
Cdd:PHA03247 2856 VAPggdvrrRPPSRSPAAKPAAPARPPVR-RLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ 2930
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
 8-70 5.57e-03

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 38.61  E-value: 5.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILPKRG--SEG-GVAAFVDFVDI----KSAQKAHNSVNKMG 70
Cdd:cd12672     8 VFVGGIDIRMDENEIRSFFARYGSVKEVKIITDRTgvSKGyGFVSFYDDVDIqkivESQINFHGKKLKLG 77
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 521-589 5.64e-03

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 38.15  E-value: 5.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568931674  521 VWLDGLSSNVSDQYLTRHFCRYGPVVKVVFDRLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12262     6 VYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYG 74
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 14-78 5.75e-03

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 38.19  E-value: 5.75e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674   14 PENVREEKIIEHFKRYGRVESVKIlpKRGseggvAAFVDFVDIKSAQKAHNSVN--KMGDRDLRTDY 78
Cdd:cd12233     9 PGTTREEDIEKLFEPFGPLVRCDI--RKT-----FAFVEFEDSEDATKALEALHgsRIDGSVLTVEF 68
RRM_ENOX cd12228
RNA recognition motif (RRM) found in the cell surface Ecto-NOX disulfide-thiol exchanger ...
 436-511 5.82e-03

RNA recognition motif (RRM) found in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins; This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs.


Pssm-ID: 409675 [Multi-domain]  Cd Length: 84  Bit Score: 38.56  E-value: 5.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  436 PKATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKVNgvpqYAFLQYCDIASVCKAIkkmdgeYLGNNRLKLG 511
Cdd:cd12228     3 PPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSKKN----FCHIRFAEEFAVDKAI------YLSGYRVRLG 68
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 8-67 6.04e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 38.38  E-value: 6.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKILpkRGSEGGVA---AFVDFVDIKSAQKAHNSVN 67
Cdd:cd12284     1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQ--KDPETGRSkgyGFIQFRDAEDAKKALEQLN 61
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
 449-505 6.12e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 38.45  E-value: 6.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  449 KTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGN 505
Cdd:cd12366    12 KSVTEDDLREAFSPFGEIQDIWVvkdKQTKESKGIAYVKFAKSSQAARAMEEMHGKCLGD 71
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
 10-62 6.20e-03

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 38.04  E-value: 6.20e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568931674   10 VGNLPENVREEKIIEHFKRYGRVESVKILPKRGSEGGVAAfVDFVDIKSAQKA 62
Cdd:cd21605     6 VGNLPFDCTWEDLKDHFSQVGEVIRADIVTSRGRHRGMGT-VEFTNKEDVDRA 57
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
 535-589 6.22e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 38.51  E-value: 6.22e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  535 LTRHFCRYGPVVKVVFD------RLKGMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFA 589
Cdd:cd12312    17 LRREFGRYGPIVDVYIPldfytrRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77
RRM1_MEI2_fungi cd12525
RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds ...
 438-482 6.31e-03

RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.


Pssm-ID: 409945 [Multi-domain]  Cd Length: 91  Bit Score: 38.53  E-value: 6.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568931674  438 ATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKV--NGVPQYAF 482
Cdd:cd12525     6 PTRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKLlsKGIVIVSF 52
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 1633-1743 6.37e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 42.39  E-value: 6.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1633 PKTPEPAAETKEPEPkAPVSAGLPAVTVTVVTPEPASSAPEKAEEAAEAPSPAGEKPAEPAPVSEetkLVSEPASVPVEQ 1712
Cdd:PRK14951  381 PARPEAAAPAAAPVA-QAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAA---VALAPAPPAQAA 456

                          90       100       110
                  ....*....|....*....|....*....|.
gi 568931674 1713 PRQSDVPPGEDSRDSQDSAALAPSAPQESAA 1743
Cdd:PRK14951  457 PETVAIPVRVAPEPAVASAAPAPAAAPAAAR 487
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
 442-504 6.38e-03

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 37.97  E-value: 6.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI------KKVNGvpqYAFLQYCDIASVCKAIKKMD-GEYLG 504
Cdd:cd12347     1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIpldyetEKHRG---FAFVEFEEAEDAAAAIDNMNeSELFG 67
RRM_RBM44 cd12248
RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; ...
 525-586 6.51e-03

RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells.


Pssm-ID: 409694 [Multi-domain]  Cd Length: 77  Bit Score: 37.97  E-value: 6.51e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  525 GLSSNVSDQYLTRHFCRYGpVVKVVFDRLK---GMALVLYSEIEDAQAAVKETKGRKIGGNKIKV 586
Cdd:cd12248     8 NLAPSVSEEDLLMHFEKYH-VSKISIQKLSmnyRYASLTFDDASDAQAAVKEMNGKDISGRKVKV 71
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
 441-511 6.84e-03

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 37.98  E-value: 6.84e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674  441 TLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQ-YAFLQYCDIASVCKAIKKMDGEYLGNNRLKLG 511
Cdd:cd12412     4 RIFVGGIDWDTTEEELREFFSKFGKVKDVKIiKDRAGVSKgYGFVTFETQEDAEKIQKWGANLVFKGKKLNVG 76
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 128-596 6.89e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.19  E-value: 6.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   128 RYERRLdgasdnRERAYEHSAYGHHERgtgafDRTRHYDQDYYRDPRERTLQHGLYYTSRSRSPNRFDAhdprYEPRARE 207
Cdd:TIGR01642    3 EEPDRE------REKSRGRDRDRSSER-----PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS----RSPRSLR 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   208 QFTLPSVVHRDIYRD-DITREVRGRRPERSyqhsrsrsphssqsrnQSPQRLASQASRPTRSPSGSGSRSRSSSSDSISS 286
Cdd:TIGR01642   68 YSSVRRSRDRPRRRSrSVRSIEQHRRRLRD----------------RSPSNQWRKDDKKRSLWDIKPPGYELVTADQAKA 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   287 SSSSSSNTDSSDSSSTASDDSPARSVQSAAVPAPtsqllsSLEKDEPRKSFGIKVQNLPVRSTDTSLKDGLFHEFKKFGK 366
Cdd:TIGR01642  132 SQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVL------PYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGY 205

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   367 --------VTSVQIHgaSEERYGLVFFRQQEDQEKALtASKGKLFFGMQIEV----------TAWVGPETESENEFRPLD 428
Cdd:TIGR01642  206 hkaedgkhVSSVNIN--KEKNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIrrphdyipvpQITPEVSQKNPDDNAKNV 282

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   429 ERIDEFH--PKATRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKK--VNGVPQ-YAFLQYCDIASVCKAIKKMDGEYL 503
Cdd:TIGR01642  283 EKLVNSTtvLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKdiATGLSKgYAFCEYKDPSVTDVAIAALNGKDT 362

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674   504 GNNRL---KLGFGKSMPT-------------------NCVWLDGLSSNV--------------SDQY------LTRHFCR 541
Cdd:TIGR01642  363 GDNKLhvqRACVGANQATidtsngmapvtllakalsqSILQIGGKPTKVvqltnlvtgddlmdDEEYeeiyedVKTEFSK 442

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568931674   542 YGPVVKVVFDRLK---------GMALVLYSEIEDAQAAVKETKGRKIGGNKIKVDFANRESQLA 596
Cdd:TIGR01642  443 YGPLINIVIPRPNgdrnstpgvGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDCYKA 506
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1645-1873 7.13e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.28  E-value: 7.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1645 PEPKAPVSAGLPAVTVTV---VTPEPASSAPEKAEEAAEAPSPAGEkPAEPAPVSEETKLVSEPASVPVEQPRQSDVPPG 1721
Cdd:PRK07764  590 PAPGAAGGEGPPAPASSGppeEAARPAAPAAPAAPAAPAPAGAAAA-PAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1722 EDSRDSQDSAALAPSAPQESAATDAVPCVNAEPLTPGTTVSQVESSVDPKPSSPQPlskltqRSEEAEEGKVEKPDTTPS 1801
Cdd:PRK07764  669 WPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQA------AQGASAPSPAADDPVPLP 742

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674 1802 TEPDAtQNAGVASEAQPPASEDVEANPPVAAKDRKTNKSKRSKTSVQAAAAsvVEKPVTRKSERIDREKLKR 1873
Cdd:PRK07764  743 PEPDD-PPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPS--MDDEDRRDAEEVAMELLEE 811
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 12-72 7.19e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 37.92  E-value: 7.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674   12 NLPENVREEKIIEHFKRYG-RVESVKIL-PKRGSEGGVAaFVDFVDIKSAQKA---HNSvnKMGDR 72
Cdd:cd12254     6 GLPFSATEEDIRDFFSGLDiPPDGIHIVyDDDGRPTGEA-YVEFASEEDAQRAlrrHKG--KMGGR 68
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 2167-2330 7.32e-03

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 41.89  E-value: 7.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2167 APPEGTQLARQIELEQAVQNIAKLPEPSAAAAskgtaTATAASEEPAPEHGHKPAHQASETELAAAIGSIISDASGEPEN 2246
Cdd:PRK13108  274 LAPKGREAPGALRGSEYVVDEALEREPAELAA-----AAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAES 348

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2247 FSAPPSVPPGSQTHPREGMEPGLHEAESGILEtgtATESSAPQVSALDPPE--GSADTKETRGNSGDSVQEAKGSKVEVT 2324
Cdd:PRK13108  349 VVQVADRDGESTPAVEETSEADIEREQPGDLA---GQAPAAHQVDAEAASAapEEPAALASEAHDETEPEVPEKAAPIPD 425


                  ....*.
gi 568931674 2325 PPRKDK 2330
Cdd:PRK13108  426 PAKPDE 431
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 8-68 7.56e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 38.06  E-value: 7.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGGVA--AFVDFVDIKSAQKAHNSVNK 68
Cdd:cd12564     3 LIVKNLPSSITEDRLRKLFSAFGTITDVQL--KYTKDGKFRrfGFVGFKSEEEAQKALKHFNN 63
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 440-514 7.66e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 37.61  E-value: 7.66e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  440 RTLFIGNLEKTTTYHDLRNIFQRFGEivdidIKKVNGVPQYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGK 514
Cdd:cd12251     2 KVLYVRNLMLSTTEEKLRELFSEYGK-----VERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAK 71
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
 8-71 7.91e-03

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 37.98  E-value: 7.91e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674    8 LWVGNLPENVREEKIIEHFKRYGRVESVKiLPKR--GSEGGVaAFVDFVdikSAQKAHNSVNKMGD 71
Cdd:cd12320     3 LIVKNVPFEATRKEIRELFSPFGQLKSVR-LPKKfdGSHRGF-AFVEFV---TKQEAQNAMEALKS 63
RRM1_SNF cd12476
RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF ...
 437-500 8.00e-03

RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 409905 [Multi-domain]  Cd Length: 85  Bit Score: 37.97  E-value: 8.00e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568931674  437 KATRTLFIGNLEKTTTYHDLRN----IFQRFGEIVDIDIKKVNGVPQYAFLQYCDIASVCKAIKKMDG 500
Cdd:cd12476     4 RPNQTIYINNLNEKVKKEELKKslyaIFSQFGQILDIVALKTLKMRGQAFVIFKDISSATNALRSMQG 71
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
 4-69 8.22e-03

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 38.08  E-value: 8.22e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    4 ETRHLWVGNLPENVREEKIIEHFKRYGRVESVKILPKR-GSEGGVaAFVDFVDIKSAQKAhnsVNKM 69
Cdd:cd12392     1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRnGKPKGL-AYVEYENEADASQA---VLKT 63
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1936-2203 8.46e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.17  E-value: 8.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 1936 RSPAKEPVEQPRVTRKRlerelQEAVVPPTTPRRGRPPKTRRRAEedgeherkePAETPRPAEGWRSPRSQKSAAAAGPQ 2015
Cdd:PRK12323  375 ATAAAAPVAQPAPAAAA-----PAAAAPAPAAPPAAPAAAPAAAA---------AARAVAAAPARRSPAPEALAAARQAS 440

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2016 GKRGRNEQKVEAAAEAGAQASTREGNPKSRGEREAASEPKRDRRDPSTDKNGPDTFPveVLERKPPEKtykskrgrARST 2095
Cdd:PRK12323  441 ARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP--PWEELPPEF--------ASPA 510

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568931674 2096 RSAMDRAAHQRSLEMAARAAGQAADKEAGPAAASPQESESPQKGSGSSPQLANNPADPDREAEEESASAS------TAPP 2169
Cdd:PRK12323  511 PAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMFDGDwpalaaRLPV 590

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 568931674 2170 EG--TQLARQIELEQAVQNIAKLPEPSAAAASKGTA 2203
Cdd:PRK12323  591 RGlaQQLARQSELAGVEGDTVRLRVPVPALAEAEVV 626
RRM1_MEI2_EAR1_like cd12275
RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 5-66 8.56e-03

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 240721 [Multi-domain]  Cd Length: 71  Bit Score: 37.54  E-value: 8.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568931674    5 TRHLWVGNLPENVREEKIIEHFKRYGRVESVKIlpKRGSEGGVaaFVDFVDIKSAQKAHNSV 66
Cdd:cd12275     1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQT--ERISEGIV--TVHFYDIRDAKRAVREL 58
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
 442-495 9.05e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 37.63  E-value: 9.05e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDI---KKVNGVPQYAFLQYCDIASVCKAI 495
Cdd:cd12328     2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIvtdKETGKKRGFAFVTFDDHDSVDKIV 58
RRM_Nab3p cd12342
RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) ...
 442-515 9.10e-03

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.


Pssm-ID: 240788 [Multi-domain]  Cd Length: 71  Bit Score: 37.42  E-value: 9.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568931674  442 LFIGNLE-KTTTYHDLRNIFQRFGEIVDIDIKKVngvpqYAFLQYCDIASVCKAIKKMDGEYLGNNRLKLGFGKS 515
Cdd:cd12342     2 LFIGNLPtKRVSKEDLFRIFSPYGHLMQIVIKNA-----FGFVQFDSPQSCRNAIECEQGEMNRGKKLHLEVSKS 71
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 339-410 9.35e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 37.54  E-value: 9.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568931674  339 IKVQNLPVRSTDTSLKDglfhEFKKFGKVTSVQI----HGASEeRYGLVFFRQQEDQEKALTASKGKLFFGMQIEV 410
Cdd:cd12565     3 IIVKNLPKYVTEKRLKE----HFSKKGEITDVKVmrtkDGKSR-RFGFIGFKSEEEAQKAVKYFNKTFIDTSKISV 73
RRM1_RBM4 cd12606
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
 442-498 9.42e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410018 [Multi-domain]  Cd Length: 67  Bit Score: 37.48  E-value: 9.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674  442 LFIGNLEKTTTYHDLRNIFQRFGEIVDIDIKKvngvpQYAFLQYCDIASVCKAIKKM 498
Cdd:cd12606     3 LFIGNLPREATEEEIRSLFEQYGKVTECDIIK-----NYGFVHMEDKSAADEAIRNL 54
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 8-78 9.44e-03

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 37.51  E-value: 9.44e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568931674    8 LWVGNLPENVREEKIIEH----FKRYGRVESVKILPKRGSEGgvAAFVDFVDIKSAQKAHNSVNKMG--DRDLRTDY 78
Cdd:cd12246     2 LYINNLNEKIKKDELKRSlyalFSQFGPVLDIVASKSLKMRG--QAFVVFKDVESATNALRALQGFPfyGKPMRIQY 76
RRM1_MEI2_EAR1_like cd12275
RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 439-508 9.54e-03

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 240721 [Multi-domain]  Cd Length: 71  Bit Score: 37.54  E-value: 9.54e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568931674  439 TRTLFIGNLEKTTTYHDLRNIFQRFGEIVDIDI-KKVNGVPQYAFLqycDIASVCKAIKKMDGEYLGNNRL 508
Cdd:cd12275     1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTeRISEGIVTVHFY---DIRDAKRAVRELCGRHMQQQAL 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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