Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078   195 DQIRQSVRHSLKDILMKRLTDSNlkipEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 274
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 568906078   275 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 308
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  1207 RERH-----DKDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDgKSADKKPDRPKgedh 1281
Cdd:TIGR01622    7 RERLrdsssAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRY-RPREKRRRRGD---- 81

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 568906078  1282 EKEKERDKSKHKEgEKDRERYHKDRDHTDRVKSKR 1316
Cdd:TIGR01622   82 SYRRRRDDRRSRR-EKPRARDGTPEPLTEDERDRR 115

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078   471 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 550
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568906078   551 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAadkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 619
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVIHAKSADVKDLYLFPPCE---FLELLLPV-GLSLEVSEPNLLLGVVVRK 142

Domain in the central regions of transcription elongation factor S-II (and elsewhere);

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078    199 QSVRHSLKDILMKRLTDSNLKIPEE-KAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 277
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 568906078    278 DHLIRMSPEELASKELAAWRRR 299
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078   118 IKKWQLAPLRKLSQPHLPRrsseekseKIAKESTALASTGERVARSGTHEKQETKKKKmeKGGPNVHPPAATSKP-SADQ 196
Cdd:TIGR01385   68 IKSWKKVVDKNKSDHPGGN--------PEDKTTVGESVNSVKQEAKSQSDKIEQPKYV--SSSPRNAKNDFVPTAvTNDK 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078   197 IRQSVRHSLKDILMKRLTDS-NLKIPEEKAAKvatkIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEV 275
Cdd:TIGR01385  138 VRDKCRELLYDALAKDSDHPpQSIDPEAKAIQ----IEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEI 213

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 568906078   276 TPDHLIRMSPEELASKELaawRRRENRHTIEMIEKEQREVERRPIT 321
Cdd:TIGR01385  214 TPEKLATMTAEEMASAEL---KQEREEITKENLFEAQGAKIQKAVT 256

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.

                            10        20        30
                    ....*....|....*....|....*....|....*...
gi 568906078      1 MVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCVRC 38
Cdd:smart00249   14 LLQCDGCDRWYHQTCLGPPLL----EEEPDGKWYCPKC 47

capsid maturational protease; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  274 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEI--EIESDAPMKEQEA 342
Cdd:PHA03369  444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIkkIAESEFKNAGAKT 523

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  343 AIEIQEPSANKSMEKPDvsekQKEEVDSTSKDTTSQHRQhlfdlncKICIGRMAPPIDDLSPKTVKVVVGGARkhSDNEA 422
Cdd:PHA03369  524 AAANIEPNCSADAAAPA----TKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568906078  423 ESLADALSSTTNILTSDL--FEEEKQESP--KSTFSPTPRPEMPGTVEVESTFLARL 475
Cdd:PHA03369  591 EALAGAIETLLTQASAQPagLSLPAPAVPvnASTPASTPPPLAPQEPPQPGTSAPSL 647

SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3), death-inducer obliterator (Dido) variants, and similar proteins; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. This group also includes the protein products of the Dido gene that encodes three alternative splicing variants (Dido1, 2, and 3), which have been implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. The Dido gene is a bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. This model corresponds to the SPOC domain of the PHF3-like group; the SPOC domain is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  478 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 557
Cdd:cd21541     1 VWKGFISMQEVAKFVASAYHVSGPCEDLSEDLPDTLEVCGRISPEQVWDYLSKLKQSGTKEIIVIRFHPANEEEKVSYIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568906078  558 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 618
Cdd:cd21541    81 LYSYLSSRKRCGVVGNNSKHVKDMYLIPLASHQPIPQVLLPFDGPGLEETRPHMLLGIIVR 141

SPOC (Spen paralog and ortholog C-terminal) domain found in Drosophila melanogaster protein partner of Sans-fille and similar proteins; Drosophila melanogaster protein partner of Sans-fille (PPS), also called protein partner of Snf, is a homolog of human DIDO. It mediates diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing. PPS associates with spliceosomal RNAs including the U1 snRNP protein Sans-fille (Snf) to mediate sex determination gene Sex-lethal (Sxl) splicing autoregulation. Alternative splicing of the Sxl pre-mRNA determines gender during development in Drosophila, producing protein-encoding mRNAs in females but yielding inactive and truncated mRNAs in males. PPS contains a plant homeodomain (PHD) finger, Brahma and Kismet (BRK), a transcription elongation factor S-II subunit M (TFSIIM) domain, and a 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  478 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 557
Cdd:cd22581     1 VWKGTINMPDVAKFNVSAQVVSGNSDDLSLDLPKVLDVVGRIAPETVWDYIGKLKKSPTKEIVVVRLTPASEEDEMSYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568906078  558 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGL-ELHRPNLLLGLIIR 618
Cdd:cd22581    81 FFEYLSSRNRLGVIGSVSKAIKDFYILPLPKESPIPEVLLPLDGPGLfENRRPNLLLGIIVR 142

SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family; The transcription factor S-II (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. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  478 IWKGFINMPSVAKFVTKAYPVSG---SPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTE-EDQI 553
Cdd:cd21538     1 VWSGKLTMPGVASFPASARQVGGpdlSSTWWTDLLPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDSsSDKA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568906078  554 SYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRP-NLLLGLIIR 618
Cdd:cd21538    81 AFDELFDYFVSRDRYGVVGPKGLAVKDLYLVPLPAGDPLPPFLLLLDDGPGPEPRDeDLLLGVIVL 146

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078   195 DQIRQSVRHSLKDILMKRLTDSNlkipEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 274
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 568906078   275 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 308
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112

PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 38
Cdd:cd15638    14 MVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 38
Cdd:cd15552    13 MICCDRCEEWFHGDCVGITEAQGKEMEENIEEYVCPKC 50

SPOC (Spen paralog and ortholog C-terminal) domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p) and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS. It plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain which is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  478 IWKGFINMPSV-AKFVTKAYPVSGS--------PEYLTEDLPDSIQVGGRISPQTVWDYVEKIKAsgTKEICVVRFTPVT 548
Cdd:cd21542     1 VWKGTLEYPEInAEFSGKIKFVGSStklskqnvKEQQDALGDKKLEVEGRLSAETADKYLNQIMS--SRDLLVYELEPNE 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 568906078  549 E-EDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIP 593
Cdd:cd21542    79 SsEDKTNFDKLFDYLHSRERYGVLKNKPSYVKDAYLIPLSAGDKPP 124

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 38
Cdd:cd15639    17 MICCDRCEEWFHGDCVGITEARGRLLERNGEDYICPNC 54

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.

                            10        20        30
                    ....*....|....*....|....*....|....*...
gi 568906078      1 MVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCVRC 38
Cdd:smart00249   14 LLQCDGCDRWYHQTCLGPPLL----EEEPDGKWYCPKC 47

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCVRC 38
Cdd:cd15489    15 LLQCDGCGKWFHADCLGPPLS----SFVPNGKWICPVC 48

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  1219 ERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRD---GKSADKKPDRPKGEDHEKEKERDKSKHKEG 1295
Cdd:TIGR01622    6 ERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDyyrGRERRSRSRRPNRRYRPREKRRRRGDSYRR 85

                   ....*.
gi 568906078  1296 EKDRER 1301
Cdd:TIGR01622   86 RRDDRR 91

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 568906078    2 VGCGRCDDWFHGDCVGLSLSQAqqmgEEDKEYVCVRC 38
Cdd:cd15610    18 VQCDGCEEWFHLLCVGLSPEEV----AEDEDYICPSC 50

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).

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                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQaqqmgEEDKEYVCVRC 38
Cdd:cd15522    14 MIGCDECDDWYHWECVGITDEP-----PEEDDWFCPKC 46

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  1177 GRQDQQQPDRPFNRGKGDRQRFYSDSHHLKRER-HDKDWEQESERHRHRDRSQERDRDRKSKEEAAahKDKERPRLSHGD 1255
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRsRDRERSRSRRRDRHRDRDYYRGRERRSRSRRP--NRRYRPREKRRR 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 568906078  1256 RAPDGKASRDGKSADKKPDRPKGE--DHEKEKERDK 1289
Cdd:TIGR01622   79 RGDSYRRRRDDRRSRREKPRARDGtpEPLTEDERDR 114

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.

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                  ....*....|....*....|....*....|....*....|..
gi 568906078    1 MVGCGRCDDWFHGDCVglslsqaqQMGEEDKE----YVCVRC 38
Cdd:cd16039    13 MIACDGCDEWYHFTCV--------NIPEADVElvdsFFCPPC 46

PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, is a UBR box-containing protein that belongs to the E3 ubiquitin ligase family that recognizes N-degrons or structurally related molecules for ubiquitin-dependent proteolysis or related processes through the UBR box motif. In addition to the UBR box, UBR7 also harbors a plant homeodomain (PHD) finger. The biochemical properties of UBR7 remain unclear.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQqmGEEDKEYVCVRC 38
Cdd:cd15542    19 MIQCVLCEDWFHGRHLGLTPPEPD--PDEFDEMICSGC 54

PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQQ-------MGEEDKEYVCVRC 38
Cdd:cd15606    12 MLQCELCKDWFHSSCVPLPKSSSQKkggngsgQGAKELKFLCPLC 56

PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    2 VGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVRC 38
Cdd:cd15687    18 VQCdGSCNRWFHQVCVGVSAEMA-----EKEDYICVSC 50

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 568906078    1 MVGCGRCDDWFHGDCVGLSlsqaQQMGEEDkeYVCVRC 38
Cdd:cd15550    13 MICCDKCSVWQHGDCMGID----RENIPDS--YLCEQC 44

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 568906078    5 GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVRC 38
Cdd:cd15686    23 GGCDEWFHQVCVGVSPEMA-----ENEDYICINC 51

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQQMGE--EDKEYVCVRC 38
Cdd:cd15592    18 MMQCGKCDRWVHSKCENLSDEMYEILSNlpESVAYTCINC 57

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568906078  1212 KDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDGKSADKKpDRPKGEDHEKEKERDKSK 1291
Cdd:TIGR01642    1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSR-SPRSLRYSSVRRSRDRPR 79

                           90
                   ....*....|....*
gi 568906078  1292 HKEGEKDRERYHKDR 1306
Cdd:TIGR01642   80 RRSRSVRSIEQHRRR 94

PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog protein, little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 568906078    1 MVGCGRCDDWFHGDCVGLSLSQAQQMG----EEDKEYVCVRC 38
Cdd:cd15516    12 MLQCELCQDWFHGSCVAVPRISSSPRPlawwEGDRKFLCPLC 53