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 1634229891 1208 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1287
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229891 1288 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIR 1348
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 1634229891  719 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKC 769
Cdd:cd15638      1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

capsid maturational protease; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229891 1004 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEIEIEsdapMKEQEAAM 1074
Cdd:PHA03369   444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIKKI----AESEFKNA 519

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229891 1075 EIQEPAAN--KSLEKPEGSEKQKEEVDSMSKDTTSQHRQhlfdlncKICIGRMAPPVDDLSPKKVKVVVGVARkhSDNEA 1152
Cdd:PHA03369   520 GAKTAAANiePNCSADAAAPATKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1634229891 1153 ESIADALSSTSNIlASEFFEEEKQESP-----KSTFSPAPRPEMPGTVEVESTFLARL 1205
Cdd:PHA03369   591 EALAGAIETLLTQ-ASAQPAGLSLPAPavpvnASTPASTPPPLAPQEPPQPGTSAPSL 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 1634229891 1208 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1287
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229891 1288 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIR 1348
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 1634229891  925 DQIRQSVRHSLKDILMKRLTDSNlkvpEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 1004
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1634229891 1005 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 1038
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 1634229891  719 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKC 769
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 1634229891  720 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeeDKEYVCVKC 769
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 1634229891 1931 KRERhEKEWEQESERHRRRDRSQDKDRDRKSREEghKDKERARLSHGDRGTDGKASRDsrnvdkkPDKPKSEDYEKDKER 2010
Cdd:TIGR01622    2 YRDR-ERERLRDSSSAGDRDRRRDKGRERSRDRS--RDRERSRSRRRDRHRDRDYYRG-------RERRSRSRRPNRRYR 71

                           90       100
                   ....*....|....*....|....*....
gi 1634229891 2011 EKSKHREGEKDRDRYHKDRDHTDRTKSKR 2039
Cdd:TIGR01622   72 PREKRRRRGDSYRRRRDDRRSRREKPRAR 100

Nuclear speckle splicing regulatory protein 1, RS-like domain; This domain found at the C-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55). This is the RS-like domain, that resembles the arginine/serine-rich (RS) domain in other SR proteins, interacts with two SR proteins and with target mRNA, being essential for NRP1 activity. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229891 1921 QRFYSDSHHLKRER---HEKEWEQESERHRRRDRSQDKDRDRKS-------REEGHKDKERARLSHGDRgtdgKASRDSR 1990
Cdd:pfam20427    4 ERGHGTKHHTKSSKsrgHEKREDQHQKRQSRDQESYYTDHDHRKekdshrhREASHRDSHWKRHEQEDK----LRGRDQR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1634229891 1991 nvdkkpdkpksEDYEKDKEREKSKHREGEKDRDRYHKDRDHTDRTKSKR 2039
Cdd:pfam20427   80 -----------ERNDREWKREKYSSREQERDRQRNDHDRHSEKGEKEEK 117

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 1634229891 1208 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1287
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229891 1288 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIR 1348
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 1634229891 1208 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1287
Cdd:cd21547      1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1634229891 1288 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIRQK 1350
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 1634229891 1201 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 1280
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1634229891 1281 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAtdkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 1349
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 1634229891 1208 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1287
Cdd:cd21540      1 LWEGAIQMFSIKQFGAKAYLVSGHSSQLIQALPAVIRSRGCILPESVWDYLDSIWPAEAKEMCLVRFAPAGARDSQNYRM 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229891 1288 LFAYFSSRKRYG-VAANNMkqvkDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLII 1347
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 1634229891   929 QSVRHSLKDILMKRLTDSNLKVPEE-KAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 1007
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 1634229891  1008 DHLIRMSPEELASKELAAWRRR 1029
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 1634229891  719 QCGfCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKC 769
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 1634229891  848 IKKWQLAplrkmgqpVLPRRSSEEKSEKIPKESTTVTCTGEKASKPGTHEKQEmKKKKVEKGVLNVHPAASASKPSADQI 927
Cdd:TIGR01385   68 IKSWKKV--------VDKNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDKIE-QPKYVSSSPRNAKNDFVPTAVTNDKV 138

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229891  928 RQSVRHSLKDILMKRLTDS-NLKVPEEKAAKvatkIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVT 1006
Cdd:TIGR01385  139 RDKCRELLYDALAKDSDHPpQSIDPEAKAIQ----IEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEIT 214

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1634229891 1007 PDHLIRMSPEELASKELaawRRRENRHTIEMIEKEQREVERRPIT 1051
Cdd:TIGR01385  215 PEKLATMTAEEMASAEL---KQEREEITKENLFEAQGAKIQKAVT 256

PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1634229891  723 CKKPH-GNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 769
Cdd:cd15560      4 CRTPYdESQFYIGCDRCQDWFHGRCVGILQSEAEKI----DEYVCPQC 47

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 1634229891 1208 IWKGFINMPSV-AKFVTKAYPVSGS--------PEYLTEDLPDSIQVGGRISPQTVWDYVEKIKAsgTKEICVVRFTPVT 1278
Cdd:cd21542      1 VWKGTLEYPEInAEFSGKIKFVGSStklskqnvKEQQDALGDKKLEVEGRLSAETADKYLNQIMS--SRDLLVYELEPNE 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1634229891 1279 E-EDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIP 1323
Cdd:cd21542     79 SsEDKTNFDKLFDYLHSRERYGVLKNKPSYVKDAYLIPLSAGDKPP 124

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 1634229891  723 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 769
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 1634229891  723 CKKP-HGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 769
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 1634229891  723 CKKPHGNRF-MVGCGRCDDWFHGDCVGLSLSQAqqmgEEDKEYVCVKC 769
Cdd:cd15610      7 CLKPTGDEVnWVQCDGCEEWFHLLCVGLSPEEV----AEDEDYICPSC 50

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 1634229891 1931 KRERhEKEWEQESERHRRRDRSQDKDRDRKSREEghKDKERARLSHGDRGTDGKASRDsrnvdkkPDKPKSEDYEKDKER 2010
Cdd:TIGR01622    2 YRDR-ERERLRDSSSAGDRDRRRDKGRERSRDRS--RDRERSRSRRRDRHRDRDYYRG-------RERRSRSRRPNRRYR 71

                           90       100
                   ....*....|....*....|....*....
gi 1634229891 2011 EKSKHREGEKDRDRYHKDRDHTDRTKSKR 2039
Cdd:TIGR01622   72 PREKRRRRGDSYRRRRDDRRSRREKPRAR 100

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 1634229891 1915 RGKGDRQRFYSDSHHLKRER-HEKEWEQESERHRRRDRSQDKDRDRKSREEGHKDKERARlshgdrgtdgKASRDSRNVD 1993
Cdd:TIGR01622   14 SSAGDRDRRRDKGRERSRDRsRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPR----------EKRRRRGDSY 83

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1634229891 1994 KKPDKPKSEDYEKDKEREKSKHREGEKDRDR 2024
Cdd:TIGR01622   84 RRRRDDRRSRREKPRARDGTPEPLTEDERDR 114

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 1634229891  723 CKKPHGNrFMVGCGRCDDWFHGDCVGLSLSQAQQ-------MGEEDKEYVCVKC 769
Cdd:cd15606      4 CRKPFSG-FMLQCELCKDWFHSSCVPLPKSSSQKkggngsgQGAKELKFLCPLC 56

PHD finger found in lysine-specific demethylase 7 (KDM7); 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. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1634229891  723 CKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 769
Cdd:cd15640      4 CRQPYDvNRFMIECDICKDWFHGSCVQVEEHHAADI----DLYHCPNC 47

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 1634229891  719 QCGFCKKPHGNR--FMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDKEYVCVKC 769
Cdd:cd15517      1 VCGICNLETAAVdeLWVQCDGCDKWFHQFCLGLS----NERYADEDKFKCPNC 49

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        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1634229891  720 CGFckkPHGNRFMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDkeYVCVKC 769
Cdd:cd15550      4 CGF---EHDDGFMICCDKCSVWQHGDCMGID----RENIPDS--YLCEQC 44

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 1634229891 1208 IWKGFINMPSvaKFVTK--AYPVSGSPEYLTEDLPDSIQVGGRispqTVWDYVEKIKASGtkEICVVRFTPVTEEDQISY 1285
Cdd:cd21546      1 KWSGTLAKSG--KPRCNvvAHPVSGDVAREPVSLPEVLNVSHR----TDLEEVAHKPVAR--AVLVLLFAPENESDRGAF 72

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1634229891 1286 TLLFAYFSSRKRYGVAanNMKQVKDMYLIPLG 1317
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 1634229891  732 MVGCGRCDDWFHGDCVGLSLSQAQQMGE--EDKEYVCVKC 769
Cdd:cd15508     18 MMQCSQCDHWVHAKCEGLSDEMYEILSYlpESIEYTCSLC 57

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        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1634229891  723 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVKC 769
Cdd:cd15687      7 CLQPEGEEVdWVQCdGSCNRWFHQVCVGVSAEMA-----EKEDYICVSC 50

PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. It contains a plant homeodomain (PHD) finger and a JmjC domain and plays an important role in adipogenesis. The PHD finger domain can recognize trimethylated histone H3 lysine 4 (H3K4me3). PHF2 also has dimethylated histone H3 lysine 9(H3K9me2) demethylase activity and acts as a coactivator of several metabolism-related transcription factors. Moreover, it can demethylate ARID5B and further forms a complex with demethylated ARD5B to bind the promoter regions of target genes. The overexpression of PHF2 is involved in the progression of esophageal squamous cell carcinoma (ESCC).

                           10        20        30
                   ....*....|....*....|....*....|...
gi 1634229891  723 CKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQA 754
Cdd:cd15641      4 CRLPYDvTRFMIECDACKDWFHGSCVGVEEEEA 36

Nuclear speckle splicing regulatory protein 1, RS-like domain; This domain found at the C-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55). This is the RS-like domain, that resembles the arginine/serine-rich (RS) domain in other SR proteins, interacts with two SR proteins and with target mRNA, being essential for NRP1 activity. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229891 1921 QRFYSDSHHLKRER---HEKEWEQESERHRRRDRSQDKDRDRKS-------REEGHKDKERARLSHGDRgtdgKASRDSR 1990
Cdd:pfam20427    4 ERGHGTKHHTKSSKsrgHEKREDQHQKRQSRDQESYYTDHDHRKekdshrhREASHRDSHWKRHEQEDK----LRGRDQR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1634229891 1991 nvdkkpdkpksEDYEKDKEREKSKHREGEKDRDRYHKDRDHTDRTKSKR 2039
Cdd:pfam20427   80 -----------ERNDREWKREKYSSREQERDRQRNDHDRHSEKGEKEEK 117

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 1634229891 1891 RRPERRHSDPWGRQDQQQLDRPFNRGKgDRQRFySDSHHLKRERHEKEweqeSERHRRR----DRSQDKDRDRKSREEGH 1966
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRSR-DRSRF-RDRHRRSRERSYRE----DSRPRDRrrydSRSPRSLRYSSVRRSRD 76

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1634229891 1967 KDKERAR-LSHGDRGTDGKASRDSRNVDKKPDKPKS 2001
Cdd:TIGR01642   77 RPRRRSRsVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112