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 1634229893 1120 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1199
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229893 1200 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIR 1260
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 1634229893  631 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKC 681
Cdd:cd15638      1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

capsid maturational protease; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229893  916 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEIEIEsdapMKEQEAAM 986
Cdd:PHA03369   444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIKKI----AESEFKNA 519

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229893  987 EIQEPAAN--KSLEKPEGSEKQKEEVDSMSKDTTSQHRQhlfdlncKICIGRMAPPVDDLSPKKVKVVVGVARkhSDNEA 1064
Cdd:PHA03369   520 GAKTAAANiePNCSADAAAPATKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1634229893 1065 ESIADALSSTSNIlASEFFEEEKQESP-----KSTFSPAPRPEMPGTVEVESTFLARL 1117
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 1634229893 1120 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1199
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229893 1200 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIR 1260
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 1634229893  837 DQIRQSVRHSLKDILMKRLTDSNlkvpEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 916
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1634229893  917 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 950
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 1634229893  631 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKC 681
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 1634229893  632 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeeDKEYVCVKC 681
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 1634229893 1843 KRERhEKEWEQESERHRRRDRSQDKDRDRKSREEghKDKERARLSHGDRGTDGKASRDsrnvdkkPDKPKSEDYEKDKER 1922
Cdd:TIGR01622    2 YRDR-ERERLRDSSSAGDRDRRRDKGRERSRDRS--RDRERSRSRRRDRHRDRDYYRG-------RERRSRSRRPNRRYR 71

                           90       100
                   ....*....|....*....|....*....
gi 1634229893 1923 EKSKHREGEKDRDRYHKDRDHTDRTKSKR 1951
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 1634229893 1833 QRFYSDSHHLKRER---HEKEWEQESERHRRRDRSQDKDRDRKS-------REEGHKDKERARLSHGDRgtdgKASRDSR 1902
Cdd:pfam20427    4 ERGHGTKHHTKSSKsrgHEKREDQHQKRQSRDQESYYTDHDHRKekdshrhREASHRDSHWKRHEQEDK----LRGRDQR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1634229893 1903 nvdkkpdkpksEDYEKDKEREKSKHREGEKDRDRYHKDRDHTDRTKSKR 1951
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 1634229893 1120 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1199
Cdd:cd21548      1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229893 1200 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIR 1260
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 1634229893 1120 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1199
Cdd:cd21547      1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1634229893 1200 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLIIRQK 1262
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 1634229893 1113 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 1192
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1634229893 1193 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAtdkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 1261
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 1634229893 1120 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1199
Cdd:cd21540      1 LWEGAIQMFSIKQFGAKAYLVSGHSSQLIQALPAVIRSRGCILPESVWDYLDSIWPAEAKEMCLVRFAPAGARDSQNYRM 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229893 1200 LFAYFSSRKRYG-VAANNMkqvkDMYLIPLGATDKIPHPLVPFDGPGLELHRPNLLLGLII 1259
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 1634229893   841 QSVRHSLKDILMKRLTDSNLKVPEE-KAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 919
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 1634229893   920 DHLIRMSPEELASKELAAWRRR 941
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 1634229893  631 QCGfCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVKC 681
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 1634229893  760 IKKWQLAplrkmgqpVLPRRSSEEKSEKIPKESTTVTCTGEKASKPGTHEKQEmKKKKVEKGVLNVHPAASASKPSADQI 839
Cdd:TIGR01385   68 IKSWKKV--------VDKNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDKIE-QPKYVSSSPRNAKNDFVPTAVTNDKV 138

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229893  840 RQSVRHSLKDILMKRLTDS-NLKVPEEKAAKvatkIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVT 918
Cdd:TIGR01385  139 RDKCRELLYDALAKDSDHPpQSIDPEAKAIQ----IEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEIT 214

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1634229893  919 PDHLIRMSPEELASKELaawRRRENRHTIEMIEKEQREVERRPIT 963
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 1634229893  635 CKKPH-GNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 681
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 1634229893 1120 IWKGFINMPSV-AKFVTKAYPVSGS--------PEYLTEDLPDSIQVGGRISPQTVWDYVEKIKAsgTKEICVVRFTPVT 1190
Cdd:cd21542      1 VWKGTLEYPEInAEFSGKIKFVGSStklskqnvKEQQDALGDKKLEVEGRLSAETADKYLNQIMS--SRDLLVYELEPNE 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1634229893 1191 E-EDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGATDKIP 1235
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 1634229893  635 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 681
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 1634229893  635 CKKP-HGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKC 681
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 1634229893  635 CKKPHGNRF-MVGCGRCDDWFHGDCVGLSLSQAqqmgEEDKEYVCVKC 681
Cdd:cd15610      7 CLKPTGDEVnWVQCDGCEEWFHLLCVGLSPEEV----AEDEDYICPSC 50

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 1634229893  631 QCGFCKKPHGN-RFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVKCCA 683
Cdd:cd15613      1 QCGSCGGNYTAdEFWICCDVCEKWYHGKCVKITPAKAEHI----KQYKCPSCSN 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 1634229893 1827 RGKGDRQRFYSDSHHLKRER-HEKEWEQESERHRRRDRSQDKDRDRKSREEGHKDKERARlshgdrgtdgKASRDSRNVD 1905
Cdd:TIGR01622   14 SSAGDRDRRRDKGRERSRDRsRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPR----------EKRRRRGDSY 83

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1634229893 1906 KKPDKPKSEDYEKDKEREKSKHREGEKDRDR 1936
Cdd:TIGR01622   84 RRRRDDRRSRREKPRARDGTPEPLTEDERDR 114

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 1634229893 1843 KRERHEKEWEQESERHRRRDRSQDKDRDRKSREEGHKDKERARlshgdrgtdGKASRDSRNVDKKPDKPKSEDYEKDKER 1922
Cdd:TIGR01642   11 KSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPR---------DRRRYDSRSPRSLRYSSVRRSRDRPRRR 81

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1634229893 1923 EKS-----KHREGEKDRDRYHKDRDHTDRTKSK 1950
Cdd:TIGR01642   82 SRSvrsieQHRRRLRDRSPSNQWRKDDKKRSLW 114

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 1634229893 1859 RRRDRSQDKDRDrkSREEGHKDKERARLSHGDRgtDGKASRDsRNVDKKPDKPKSEDYEKDKEREKSKHREGEKDRDRyH 1938
Cdd:TIGR01622    1 RYRDRERERLRD--SSSAGDRDRRRDKGRERSR--DRSRDRE-RSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPR-E 74

                           90
                   ....*....|...
gi 1634229893 1939 KDRDHTDRTKSKR 1951
Cdd:TIGR01622   75 KRRRRGDSYRRRR 87

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 1634229893  635 CKKPH------GNRFMVGCGRCDDWFHGDCVGLSLSQAQqmGEEDKEYVCVKC 681
Cdd:cd15542      4 CDRPYpdpedeVEDEMIQCVLCEDWFHGRHLGLTPPEPD--PDEFDEMICSGC 54

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 1634229893  632 CGFckkPHGNRFMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDkeYVCVKC 681
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 1634229893 1120 IWKGFINMPSvaKFVTK--AYPVSGSPEYLTEDLPDSIQVGGRispqTVWDYVEKIKASGtkEICVVRFTPVTEEDQISY 1197
Cdd:cd21546      1 KWSGTLAKSG--KPRCNvvAHPVSGDVAREPVSLPEVLNVSHR----TDLEEVAHKPVAR--AVLVLLFAPENESDRGAF 72

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1634229893 1198 TLLFAYFSSRKRYGVAanNMKQVKDMYLIPLG 1229
Cdd:cd21546     73 DEFIDYLSSKDRAGVV--KLPDNRTLYLVPPS 102

PHD finger found in histone lysine demethylase PHF8; 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. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1634229893  634 FCKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQM 669
Cdd:cd15642      4 LCRLPYDvTRFMIECDVCQDWFHGSCVGVEEEKAAEI 40

PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1634229893  634 FCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedkeYVCVKC 681
Cdd:cd15632      5 FCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV------YVCQKC 46

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 1634229893  635 CKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQA 666
Cdd:cd15641      4 CRLPYDvTRFMIECDACKDWFHGSCVGVEEEEA 36

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 1634229893  634 FCKKPHGNrFMVGCGRCDDWFHGDCVGlslsQAQQMGEEDKEYVCVKC 681
Cdd:cd15518      3 FCRQGEGG-TMIECEICKEWYHVKCIK----NGRWKLDDDDKFVCPIC 45

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 1634229893 1833 QRFYSDSHHLKRER---HEKEWEQESERHRRRDRSQDKDRDRKS-------REEGHKDKERARLSHGDRgtdgKASRDSR 1902
Cdd:pfam20427    4 ERGHGTKHHTKSSKsrgHEKREDQHQKRQSRDQESYYTDHDHRKekdshrhREASHRDSHWKRHEQEDK----LRGRDQR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1634229893 1903 nvdkkpdkpksEDYEKDKEREKSKHREGEKDRDRYHKDRDHTDRTKSKR 1951
Cdd:pfam20427   80 -----------ERNDREWKREKYSSREQERDRQRNDHDRHSEKGEKEEK 117

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 1634229893  635 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVKC 681
Cdd:cd15686      8 CQRPCKDKVdWVQCdGGCDEWFHQVCVGVSPEMA-----ENEDYICINC 51