SPOC (Spen paralog and ortholog C-terminal) domain 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 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 1720354567 1133 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1212
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720354567 1213 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1273
Cdd:cd21548     81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLIIR 141

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        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720354567  643 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 693
Cdd:cd15638      1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

capsid maturational protease; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567  929 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEI--EIESDAPMKEQEA 997
Cdd:PHA03369   444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIkkIAESEFKNAGAKT 523

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567  998 AIEIQEPSANKSMEKPDvsekQKEEVDSTSKDTTSQHRQhlfdlncKICIGRMAPPIDDLSPKTVKVVVGGARkhSDNEA 1077
Cdd:PHA03369   524 AAANIEPNCSADAAAPA----TKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720354567 1078 ESLADALSSTTNILTSDL--FEEEKQESP--KSTFSPTPRPEMPGTVEVESTFLARL 1130
Cdd:PHA03369   591 EALAGAIETLLTQASAQPagLSLPAPAVPvnASTPASTPPPLAPQEPPQPGTSAPSL 647

SPOC (Spen paralog and ortholog C-terminal) domain 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 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 1720354567 1133 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1212
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720354567 1213 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1273
Cdd:cd21548     81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLIIR 141

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 1720354567  850 DQIRQSVRHSLKDILMKRLTDSNlkipEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 929
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1720354567  930 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 963
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        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720354567  643 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 693
Cdd:cd15638      1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1720354567  644 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeeDKEYVCVRC 693
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIP---SGEWLCPEC 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 1720354567 1862 RERH-----DKDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDgKSADKKPDRPKgedh 1936
Cdd:TIGR01622    7 RERLrdsssAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRY-RPREKRRRRGD---- 81

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1720354567 1937 EKEKERDKSKHKEgEKDRERYHKDRDHTDRVKSKR 1971
Cdd:TIGR01622   82 SYRRRRDDRRSRR-EKPRARDGTPEPLTEDERDRR 115

transcription termination factor Rho; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567 1819 DIRRPERRHSDPWGRQDQQQPDRpfnRGKGDRQRfysdshhlKRERHDKDWEQESERHRHRDRSQERDRDRKSKEEAAAH 1898
Cdd:PRK12678   108 ARAAAAAAAEAASAPEAAQARER---RERGEAAR--------RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRG 176

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720354567 1899 KDKERPRLSH-GDRAPDGKASRDGKSADKKPDRPKGEDHEKEKERDKSKHKEGEKDRERYHKDRDHTDR 1966
Cdd:PRK12678   177 DREDRQAEAErGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRE 245

SPOC (Spen paralog and ortholog C-terminal) domain 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 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 1720354567 1133 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1212
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720354567 1213 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1273
Cdd:cd21548     81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLIIR 141

SPOC (Spen paralog and ortholog C-terminal) domain found in some death-inducer obliterator variants; The Dido/DIDO1 gene has been implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. It encodes alternative splicing variants, including Dido1, 2, and 3, with Dido3 being the longest isoform and Dido1 being the shortest. Dido3 is ubiquitously expressed in all human tissues, is dispensable for embryonic stem (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. Dido2 and Dido1 are truncated at the C-terminus relative to Dido3, with Dido2 containing a partial SPOC domain whereas Dido1 is missing it completely. Dido1, also called DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining ES cells and directly regulates the expression of pluripotency factors. The conserved plant homeodomain (PHD) finger is responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). The Dido/DIDO1 gene is a bone morphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. 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 1720354567 1133 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1212
Cdd:cd21547      1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720354567 1213 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIRQK 1275
Cdd:cd21547     81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTRPNIILGLVICQK 143

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 1720354567 1126 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 1205
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720354567 1206 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAadkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 1274
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVIHAKSADVKDLYLFPPCE---FLELLLPV-GLSLEVSEPNLLLGVVVRK 142

SPOC (Spen paralog and ortholog C-terminal) domain found in SPOC domain-containing protein 1 (SPOCD1) and similar proteins; SPOCD1 is a protein belonging to the transcription factor S-II (TFIIS) family of transcription factors. It acts as a tumor-related factor that promotes cell proliferation and metastasis. SPOCD1 was initially found to interact with testis protein phosphatase 1, which is a major eukaryotic serine/threonine-specific phosphatase that regulates cellular signaling. The model corresponds to the SPOC domain of SPOCD1; 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 1720354567 1133 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1212
Cdd:cd21540      1 LWEGAIQMFSIKQFGAKAYLVSGHSSQLIQALPAVIRSRGCILPESVWDYLDSIWPAEAKEMCLVRFAPAGARDSQNYRM 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720354567 1213 LFAYFSSRKRYG-VAANNMkqvkDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLII 1272
Cdd:cd21540     81 LYSYLNNKQRYGiVDSEKM----DMFLIPLPAFQPVPAKLRPLGGPGLEATHSSLLLALIL 137

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

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567   854 QSVRHSLKDILMKRLTDSNLKIPEE-KAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 932
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 1720354567   933 DHLIRMSPEELASKELAAWRRR 954
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102

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        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1720354567  643 QCGfCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 693
Cdd:cd15552      1 YCI-CRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMEENIEEYVCPKC 50

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 1720354567  773 IKKWQLAPLRKLSQPHLPRrsseekseKIAKESTALASTGERVARSGTHEKQETKKKKmeKGGPNVHPPAATSKP-SADQ 851
Cdd:TIGR01385   68 IKSWKKVVDKNKSDHPGGN--------PEDKTTVGESVNSVKQEAKSQSDKIEQPKYV--SSSPRNAKNDFVPTAvTNDK 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567  852 IRQSVRHSLKDILMKRLTDS-NLKIPEEKAAKvatkIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEV 930
Cdd:TIGR01385  138 VRDKCRELLYDALAKDSDHPpQSIDPEAKAIQ----IEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEI 213

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1720354567  931 TPDHLIRMSPEELASKELaawRRRENRHTIEMIEKEQREVERRPIT 976
Cdd:TIGR01385  214 TPEKLATMTAEEMASAEL---KQEREEITKENLFEAQGAKIQKAVT 256

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        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1720354567  640 PSKQCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 693
Cdd:cd15639      1 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLERNGEDYICPNC 54

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1720354567  644 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeeDKEYVCVRC 693
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIP---SGEWLCPEC 48

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720354567  647 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 693
Cdd:cd15553      4 CRSSDISRFMIGCDNCEEWYHGDCINITEKEAKAI----KEWYCQQC 46

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720354567  647 CKKP-HGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 693
Cdd:cd15554      4 CRQPyDVTRFMIECDVCKDWFHGSCVGVEEHQANDI----ERYHCPNC 47

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        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720354567  647 CKKPHGNRF-MVGCGRCDDWFHGDCVGLSLSQAqqmgEEDKEYVCVRC 693
Cdd:cd15610      7 CLKPTGDEVnWVQCDGCEEWFHLLCVGLSPEEV----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).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1720354567  644 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQaqqmgEEDKEYVCVRC 693
Cdd:cd15522      2 CPICKKPDDGSPMIGCDECDDWYHWECVGITDEP-----PEEDDWFCPKC 46

PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed nuclear proteins existing only in plants. They are involved in chromatin regulation by binding to tri- and dimethylated histone H3 at lysine 4 (H3K4me3/2), the active histone markers, through their plant homeodomain (PHD) fingers.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1720354567  643 QCGFCKKPHGN-RFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRCCA 695
Cdd:cd15613      1 QCGSCGGNYTAdEFWICCDVCEKWYHGKCVKITPAKAEHI----KQYKCPSCSN 50

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        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1720354567  647 CKKPHGNrFMVGCGRCDDWFHGDCVGLSLSQAQQ-------MGEEDKEYVCVRC 693
Cdd:cd15606      4 CRKPFSG-FMLQCELCKDWFHSSCVPLPKSSSQKkggngsgQGAKELKFLCPLC 56

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        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720354567  647 CKKPH------GNRFMVGCGRCDDWFHGDCVGLSLSQAQqmGEEDKEYVCVRC 693
Cdd:cd15542      4 CDRPYpdpedeVEDEMIQCVLCEDWFHGRHLGLTPPEPD--PDEFDEMICSGC 54

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. 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 interaction 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. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1720354567  643 QCGFCKKPHGNR--FMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDKEYVCVRC 693
Cdd:cd15517      1 VCGICNLETAAVdeLWVQCDGCDKWFHQFCLGLS----NERYADEDKFKCPNC 49

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the 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). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1720354567  647 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 693
Cdd:cd15570      4 CGSSMEDGSMIQCEGCKTWQHMDCVLIPDKPADGLPELPSKFYCELC 50

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567 1133 IWKGFINMPSvaKFVTK--AYPVSGSPEYLTEDLPDSIQVGGRispqTVWDYVEKIKASGtkEICVVRFTPVTEEDQISY 1210
Cdd:cd21546      1 KWSGTLAKSG--KPRCNvvAHPVSGDVAREPVSLPEVLNVSHR----TDLEEVAHKPVAR--AVLVLLFAPENESDRGAF 72

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1720354567 1211 TLLFAYFSSRKRYGVAanNMKQVKDMYLIPLG 1242
Cdd:cd21546     73 DEFIDYLSSKDRAGVV--KLPDNRTLYLVPPS 102

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A 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. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, 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 1720354567  656 MVGCGRCDDWFHGDCVGLSLSQAQQMGE--EDKEYVCVRC 693
Cdd:cd15508     18 MMQCSQCDHWVHAKCEGLSDEMYEILSYlpESIEYTCSLC 57

capsid maturational protease; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567  929 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEI--EIESDAPMKEQEA 997
Cdd:PHA03369   444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIkkIAESEFKNAGAKT 523

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720354567  998 AIEIQEPSANKSMEKPDvsekQKEEVDSTSKDTTSQHRQhlfdlncKICIGRMAPPIDDLSPKTVKVVVGGARkhSDNEA 1077
Cdd:PHA03369   524 AAANIEPNCSADAAAPA----TKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720354567 1078 ESLADALSSTTNILTSDL--FEEEKQESP--KSTFSPTPRPEMPGTVEVESTFLARL 1130
Cdd:PHA03369   591 EALAGAIETLLTQASAQPagLSLPAPAVPvnASTPASTPPPLAPQEPPQPGTSAPSL 647

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1720354567  646 FCKKPHGNrFMVGCGRCDDWFHGDCVGlslsQAQQMGEEDKEYVCVRC 693
Cdd:cd15518      3 FCRQGEGG-TMIECEICKEWYHVKCIK----NGRWKLDDDDKFVCPIC 45

PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1, and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. The family corresponds to the third PHD finger.

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1720354567  656 MVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 693
Cdd:cd15520     14 MIFCDRCERTVHLDCVGLSDRIVDSP----SEFFCPEC 47

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        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1720354567  647 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVRC 693
Cdd:cd15686      8 CQRPCKDKVdWVQCdGGCDEWFHQVCVGVSPEMA-----ENEDYICINC 51

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 1720354567 1867 KDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDGKSADKKpDRPKGEDHEKEKERDKSK 1946
Cdd:TIGR01642    1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSR-SPRSLRYSSVRRSRDRPR 79

                           90
                   ....*....|....*
gi 1720354567 1947 HKEGEKDRERYHKDR 1961
Cdd:TIGR01642   80 RRSRSVRSIEQHRRR 94