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Conserved domains on  [gi|1907156742|ref|XP_036020174|]
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serine/arginine-rich splicing factor 4 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
1-52 3.13e-25

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).


The actual alignment was detected with superfamily member cd12600:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 72  Bit Score: 97.15  E-value: 3.13e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED 52
Cdd:cd12600    21 MRQAGEVTYADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKIRLVED 72
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
122-234 8.96e-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: 37.95  E-value: 8.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156742 122 EKSRSPSKD-NKSRSRSRSPDKSRSKSKDHaedklqnndSAGKAKSHSPSRHDSKSRSRSQERRAEEERRRSVSRARSQE 200
Cdd:TIGR01642  10 EKSRGRDRDrSSERPRRRSRDRSRFRDRHR---------RSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907156742 201 KSRSQeKSLLKSRSRSRSKVGSRSRSRSKDKRKG 234
Cdd:TIGR01642  81 RSRSV-RSIEQHRRRLRDRSPSNQWRKDDKKRSL 113
 
Name Accession Description Interval E-value
RRM2_SRSF4_like cd12600
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
1-52 3.13e-25

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM2 of 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 is 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: 410012 [Multi-domain]  Cd Length: 72  Bit Score: 97.15  E-value: 3.13e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED 52
Cdd:cd12600    21 MRQAGEVTYADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKIRLVED 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
2-48 9.74e-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: 45.69  E-value: 9.74e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907156742   2 RQAGEVTYA----DAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIR 48
Cdd:pfam00076  20 SKFGPIKSIrlvrDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
1-49 6.67e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.35  E-value: 6.67e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907156742    1 MRQAGEVTYA----DAHKGR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRL 49
Cdd:smart00360  20 FSKFGKVESVrlvrDKETGKsKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
3-54 2.10e-04

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 39.70  E-value: 2.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156742   3 QAGEVTYA----DAHKGR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKP 54
Cdd:COG0724    24 EYGEVTSVklitDRETGRsRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARP 80
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
122-234 8.96e-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: 37.95  E-value: 8.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156742 122 EKSRSPSKD-NKSRSRSRSPDKSRSKSKDHaedklqnndSAGKAKSHSPSRHDSKSRSRSQERRAEEERRRSVSRARSQE 200
Cdd:TIGR01642  10 EKSRGRDRDrSSERPRRRSRDRSRFRDRHR---------RSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907156742 201 KSRSQeKSLLKSRSRSRSKVGSRSRSRSKDKRKG 234
Cdd:TIGR01642  81 RSRSV-RSIEQHRRRLRDRSPSNQWRKDDKKRSL 113
 
Name Accession Description Interval E-value
RRM2_SRSF4_like cd12600
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
1-52 3.13e-25

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM2 of 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 is 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: 410012 [Multi-domain]  Cd Length: 72  Bit Score: 97.15  E-value: 3.13e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED 52
Cdd:cd12600    21 MRQAGEVTYADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKIRLVED 72
RRM2_SRSF6 cd12766
RNA recognition motif 2 (RRM2) found found in vertebrate serine/arginine-rich splicing factor ...
1-53 6.25e-24

RNA recognition motif 2 (RRM2) found found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subgroup corresponds to the RRM2 of SRSF6, also termed pre-mRNA-splicing factor SRp55, an essential splicing regulatory serine/arginine (SR) protein that 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. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 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.


Pssm-ID: 410159 [Multi-domain]  Cd Length: 73  Bit Score: 93.56  E-value: 6.25e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDK 53
Cdd:cd12766    21 MRQAGEVTYADAHKERTNEGVIEFRSYSDMKRALEKLDGTEINGRKIRLVEDK 73
RRM2_SRSF1_4_like cd12339
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and ...
1-50 5.44e-20

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins; This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of 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). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It 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 with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409776 [Multi-domain]  Cd Length: 70  Bit Score: 82.64  E-value: 5.44e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLV 50
Cdd:cd12339    21 MRKAGEVTYADVHRDREGEGVVEFTSEEDMKRAIEKLDGTEFNGRRIRVE 70
RRM2_SRSF4 cd12764
RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 4 ...
1-65 2.22e-17

RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 4 (SRSF4); This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 410157 [Multi-domain]  Cd Length: 97  Bit Score: 76.72  E-value: 2.22e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKPGSRRRRSYSRS 65
Cdd:cd12764    33 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKPGSRRRRSYSRS 97
RRM2_SRSF5 cd12765
RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 5 ...
1-51 3.19e-14

RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM2 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5), 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: 410158 [Multi-domain]  Cd Length: 81  Bit Score: 67.42  E-value: 3.19e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907156742   1 MRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVE 51
Cdd:cd12765    30 MRQAGEVTFADAHRPKLNEGVVEFASYSDLKNAIEKLSGKEINGRKIKLIE 80
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
2-48 9.74e-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: 45.69  E-value: 9.74e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907156742   2 RQAGEVTYA----DAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIR 48
Cdd:pfam00076  20 SKFGPIKSIrlvrDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM2_SRSF1_like cd12601
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF9 and ...
1-41 1.82e-06

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins; This subfamily corresponds to the RRM2 of serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins. SRSF1, also termed ASF-1, 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, also termed SRp30C, 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. 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.


Pssm-ID: 410013 [Multi-domain]  Cd Length: 74  Bit Score: 45.19  E-value: 1.82e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907156742   1 MRQAGEVTYADAHkgRKNEGVIEFVSYSDMKRALEKLDGTE 41
Cdd:cd12601    21 MREAGDVCYADVY--RDGTGVVEFLRYEDMKYAVRKLDDSK 59
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
1-49 2.41e-06

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: 44.58  E-value: 2.41e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907156742   1 MRQAGEVTYA----DAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRL 49
Cdd:cd00590    19 FSKFGEVVSVrivrDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM smart00360
RNA recognition motif;
1-49 6.67e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.35  E-value: 6.67e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1907156742    1 MRQAGEVTYA----DAHKGR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRL 49
Cdd:smart00360  20 FSKFGKVESVrlvrDKETGKsKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM2_SF2_plant_like cd12602
RNA recognition motif 2 (RRM2) found in plant pre-mRNA-splicing factor SF2 and similar ...
1-41 7.57e-06

RNA recognition motif 2 (RRM2) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subfamily corresponds to the RRM2 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: 410014 [Multi-domain]  Cd Length: 76  Bit Score: 43.67  E-value: 7.57e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1907156742   1 MRQAGEVTYADAHK-GRKNEGVIEFVSYSDMKRALEKLDGTE 41
Cdd:cd12602    21 MRRAGEVCFSQVFRdGRGTTGVVDYTTYDDMKYAIRKLDDTE 62
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
3-52 4.59e-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: 41.13  E-value: 4.59e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907156742   3 QAGEVTYAD--AHKGR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED 52
Cdd:cd21605    24 QVGEVIRADivTSRGRhRGMGTVEFTNKEDVDRAISKFDHTMFMGREIFVRQD 76
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
3-54 2.10e-04

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 39.70  E-value: 2.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907156742   3 QAGEVTYA----DAHKGR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKP 54
Cdd:COG0724    24 EYGEVTSVklitDRETGRsRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARP 80
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
5-49 9.42e-04

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: 37.61  E-value: 9.42e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907156742   5 GEVTYADAHK----GR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRL 49
Cdd:cd12284    23 GKIEFVQLQKdpetGRsKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKV 72
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
14-47 1.13e-03

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 37.38  E-value: 1.13e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1907156742  14 KGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKI 47
Cdd:cd12407    37 RGSKGFGFVTFANSADADRAREKLNGTVVEGRKI 70
RRM1_hnRNPM_like cd12385
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
2-52 2.37e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409819 [Multi-domain]  Cd Length: 76  Bit Score: 36.24  E-value: 2.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907156742   2 RQAGEVTYA----DAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED 52
Cdd:cd12385    22 EKVGEVTYVelfkDENGKSRGCGIVEFKDLESVQKALETMNRYELKGRKLVVKED 76
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
11-48 7.14e-03

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: 35.28  E-value: 7.14e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907156742  11 DAHKGR-KNEGVIEFVSYSDMKRALEKLDGTEVNGRKIR 48
Cdd:cd12363    36 DQQTGRsRGFGFVYFESVEDAKEAKERLNGQEIDGRRIR 74
RRM1_hnRNPM cd12657
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
3-52 8.43e-03

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410058 [Multi-domain]  Cd Length: 76  Bit Score: 34.87  E-value: 8.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907156742   3 QAGEVTYA----DAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED 52
Cdd:cd12657    23 KVGEVTYVellmDAEGKSRGCAVVEFKTEESMKKAVEVLNKHSFNGRPLKVKED 76
RRM2_SRSF1 cd12767
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
1-41 8.76e-03

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM2 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit, 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 SR domains rich in serine-arginine dipeptides.


Pssm-ID: 410160 [Multi-domain]  Cd Length: 84  Bit Score: 35.09  E-value: 8.76e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907156742   1 MRQAGEVTYADAHkgRKNEGVIEFVSYSDMKRALEKLDGTE 41
Cdd:cd12767    29 MREAGDVCYADVF--RDGTGVVEFVRKEDMTYAVRKLDNTK 67
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
122-234 8.96e-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: 37.95  E-value: 8.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907156742 122 EKSRSPSKD-NKSRSRSRSPDKSRSKSKDHaedklqnndSAGKAKSHSPSRHDSKSRSRSQERRAEEERRRSVSRARSQE 200
Cdd:TIGR01642  10 EKSRGRDRDrSSERPRRRSRDRSRFRDRHR---------RSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907156742 201 KSRSQeKSLLKSRSRSRSKVGSRSRSRSKDKRKG 234
Cdd:TIGR01642  81 RSRSV-RSIEQHRRRLRDRSPSNQWRKDDKKRSL 113
 
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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