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 859821499 1047 IWKGFINMQSVAKFVTKAYPVSGCCDYLSEDLPDTIHIGGRITPRTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1126
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 859821499 1127 LYSYFSSRGRFGVVANNSRHVKDLYLIPLSAKDPVPSKLLPFEGPGLESPRPNIILGLVICQR 1189
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTRPNIILGLVICQK 143

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 859821499  262 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 315
Cdd:cd15639     1 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLERNGEDYICPNC 54

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499  859 PAPKKQKLSASKKEEPKPQYEPPPSEPVLGSaNEAMPETLPESASePDLDGAAHAHLERKYFP--VPPGDSRPEPSALEG 936
Cdd:PHA03247 2554 PLPPAAPPAAPDRSVPPPRPAPRPSEPAVTS-RARRPDAPPQSAR-PRAPVDDRGDPRGPAPPspLPPDTHAPDPPPPSP 2631

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499  937 PSCPATCGGSVLTTVTVSGRDPRTASSGSCT----VTAPAAARPDGAHPAEPRQDVLKPAVTSVT-VPKSILAKPSPSPE 1011
Cdd:PHA03247 2632 SPAANEPDPHPPPTVPPPERPRDDPAPGRVSrprrARRLGRAAQASSPPQRPRRRAARPTVGSLTsLADPPPPPPTPEPA 2711

                         170       180
                  ....*....|....*....|..
gi 859821499 1012 PRYLLPVPPAPRVSLSESRSPP 1033
Cdd:PHA03247 2712 PHALVSATPLPPGPAAARQASP 2733

Uncharacterized coiled-coil protein SlyX (sensitive to lysis X) [Function unknown];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 859821499 1468 LVEQQQMIEELNKQIEEQKRQVAEQEA---ALRQQRAAVGASMAHFSVADAlmsPPP 1521
Cdd:COG2900    12 LAFQEDTIEELNDVVARQQREIDRLQRqlrLLAERLKELEPSLGASPAEEE---PPP 65

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 859821499 1047 IWKGFINMQSVAKFVTKAYPVSGCCDYLSEDLPDTIHIGGRITPRTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1126
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 859821499 1127 LYSYFSSRGRFGVVANNSRHVKDLYLIPLSAKDPVPSKLLPFEGPGLESPRPNIILGLVICQR 1189
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTRPNIILGLVICQK 143

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

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499    664 QNIRRSLKEILWKRVNDSDDLIMTESEVGKIALHIEKEMFNLFQVTDNRYKSRYRSIMFNLKDPKNQGLFHRVLREEISS 743
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 859821499    744 AKLVRMKPEELASKELSTWRER 765
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102

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 859821499   659 NSQIRQNIRRSLKEILWKRVNDSDdlimtESEVGKIALHIEKEMFNLFQVTDNRYKSRYRSIMFNLKDPKNQGLFHRVLR 738
Cdd:pfam07500    2 GDKVRDKCRELLYDALAKDSTEAS-----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLS 76

                           90       100
                   ....*....|....*....|....*..
gi 859821499   739 EEISSAKLVRMKPEELASKELSTWRER 765
Cdd:pfam07500   77 GEISPEKLVTMSPEEMASEELKKEREK 103

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 859821499   266 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLErngEDYICPNCT 316
Cdd:pfam00628    1 YCaVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPS---GEWLCPECK 49

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1632 RPARRVLLPTPPSSAFQPGFPLQSAQSFPSPGARDPFSAPVCTAQEKCEDPRNAQFAEKGDPPAVEAEGDGEPPCRPGEG 1711
Cdd:PHA03247 2572 RPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPER 2651

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1712 AATFPSAGQ-----------RAGAPLPPSQGQREPAPRTfGTSGLHGPSFPGPRGPAPPFSEENIVSNSDGPRGPPPARF 1780
Cdd:PHA03247 2652 PRDDPAPGRvsrprrarrlgRAAQASSPPQRPRRRAARP-TVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQ 2730

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1781 GAQKGPI-PSLFSGPHGPP-PYGDSRGPSPSHLGGPRGSAPPQFEERKDPHGEKREFQDGPYDEPAGPVPQFEGAEQSQF 1858
Cdd:PHA03247 2731 ASPALPAaPAPPAVPAGPAtPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAA 2810

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1859 VGGRGAAPFQFGGQRRPLLSQFKGPRGGPPPPQFGGQRGPPPGHFVGPRGP----HPNQFEGPRGQAPNFMPGPRGVQPQ 1934
Cdd:PHA03247 2811 VLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDvrrrPPSRSPAAKPAAPARPPVRRLARPA 2890

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1935 PFEE-----QRVSSPPRFANPRAPAPLPFGGPRGSVPFPEKSEPTPPRfhfqgPPAPglkAAPRPLLELPSHPPPHRPER 2009
Cdd:PHA03247 2891 VSRStesfaLPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPR-----PQPP---LAPTTDPAGAGEPSGAVPQP 2962

                         410       420
                  ....*....|....*....|....*.
gi 859821499 2010 WDEAPVQG--PEPEFREAKGHDYRSA 2033
Cdd:PHA03247 2963 WLGALVPGrvAVPRFRVPQPAPSREA 2988

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 859821499  237 KAARGLEGR-DPRDVGRQKPECEAYEPNALYCICRQPHNNRfMICCD--RCE-EWFHGDCVGISEA 298
Cdd:COG5034   193 TATRVKEGNnGGSTKSRGVSSEDNSEGEELYCFCQQVSYGQ-MVACDnaNCKrEWFHLECVGLKEP 257

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 859821499  2086 RGHERARHRDKDAGREWDRSRERGADRDRGRDPERASEWGRSRERSRNRERERRRERERSRSRERGRDRTREHGRERKDR 2165
Cdd:TIGR01622    3 RDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPREKRRRRGDS 82

                           90       100
                   ....*....|....*....|....
gi 859821499  2166 SKSKEGSRDPKADAPRAATPAGQN 2189
Cdd:TIGR01622   83 YRRRRDDRRSRREKPRARDGTPEP 106

SlyX; The SlyX protein has no known function. It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 859821499  1471 QQQMIEELNKQIEEQKRQVAEQEA---ALRQQRAAVGASMAHFSVADAlmsPPP 1521
Cdd:pfam04102   14 QEDTIEELNDVVAEQQRQIDRLQRqlrLLAERLKELEPSLGADPAEEE---PPP 64

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 859821499 1047 IWKGFINMQSVAKFVTKAYPVSGCCDYLSEDLPDTIHIGGRITPRTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1126
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 859821499 1127 LYSYFSSRGRFGVVANNSRHVKDLYLIPLSAKDPVPSKLLPFEGPGLESPRPNIILGLVICQR 1189
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTRPNIILGLVICQK 143

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 859821499 1047 IWKGFINMQSVAKFVTKAYPVSGCCDYLSEDLPDTIHIGGRITPRTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1126
Cdd:cd21548     1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1127 LYSYFSSRGRFGVVANNSRHVKDLYLIPLSAKDPVPSKLLPFEGPGLESPRPNIILGLVI 1186
Cdd:cd21548    81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLII 140

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 859821499  1040 FLSRLSTIWKGFINMQSVAKFVTKAYPVSGCCDYLsedLPDTIHIGGRITPRTVWDYVGKLKSSVSKELCLIRFHPATEE 1119
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 859821499  1120 EEVAYISLYSYFSSRGRFGVVANNSRHVKDLYLIPLSakdPVPSKLLPfEGPGLESPRPNIILGLVICQ 1188
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVIHAKSADVKDLYLFPPC---EFLELLLP-VGLSLEVSEPNLLLGVVVRK 142

SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family; The transcription factor S-II (TFIIS) family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 859821499 1047 IWKGFINMQSVAKFVTKAYPVSGCCDYLSED---LPDTIHIGGRITPRTVWDYVGKLKSSVSKELCLIRFHPATE-EEEV 1122
Cdd:cd21538     1 VWSGKLTMPGVASFPASARQVGGPDLSSTWWtdlLPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDSsSDKA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 859821499 1123 AYISLYSYFSSRGRFGVVANNSRHVKDLYLIPLSAKDPVPSKLLPFEGPGLESPRP-NIILGLVIC 1187
Cdd:cd21538    81 AFDELFDYFVSRDRYGVVGPKGLAVKDLYLVPLPAGDPLPPFLLLLDDGPGPEPRDeDLLLGVIVL 146

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 859821499  262 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 315
Cdd:cd15639     1 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLERNGEDYICPNC 54

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 859821499  266 YCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 315
Cdd:cd15552     1 YCICRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMEENIEEYVCPKC 50

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.

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gi 859821499  266 YCICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERngedYICPNC 315
Cdd:cd15554     1 YCICRQPYDvTRFMIECDVCKDWFHGSCVGVEEHQANDIER----YHCPNC 47

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.

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gi 859821499  268 ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 315
Cdd:cd15638     4 FCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

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

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gi 859821499  266 YCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERngedYICPNC 315
Cdd:cd16039     1 YCICQKPDDGRWMIACDGCDEWYHFTCVNIPEADVELVDS----FFCPPC 46

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.

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gi 859821499   266 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLErngEDYICPNCT 316
Cdd:pfam00628    1 YCaVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPS---GEWLCPECK 49

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

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gi 859821499    266 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEargrLLERNGEDYICPNC 315
Cdd:smart00249    1 YCsVCGKPDDGGELLQCDGCDRWYHQTCLGPPL----LEEEPDGKWYCPKC 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.

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gi 859821499 1047 IWKGFINMQSV-AKFVTKAYPVSGCC--------DYLSEDLPDTIHIGGRITPRTVWDYVGKLKSSvsKELCLIRFHP-A 1116
Cdd:cd21542     1 VWKGTLEYPEInAEFSGKIKFVGSSTklskqnvkEQQDALGDKKLEVEGRLSAETADKYLNQIMSS--RDLLVYELEPnE 78

                          90       100       110       120       130       140
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gi 859821499 1117 TEEEEVAYISLYSYFSSRGRFGVVANNSRHVKDLYLIPLSAKDPVPSKLLPFEGPGLESPR 1177
Cdd:cd21542    79 SSEDKTNFDKLFDYLHSRERYGVLKNKPSYVKDAYLIPLSAGDKPPILFIILNPISILEEE 139

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.

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gi 859821499  267 CICRQPHNNRFMICCDRCEEWFHGDCVGISEargrllERNGEDYICPNC 315
Cdd:cd15550     2 CICGFEHDDGFMICCDKCSVWQHGDCMGIDR------ENIPDSYLCEQC 44

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).

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gi 859821499  266 YCICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERngedYICPNC 315
Cdd:cd15641     1 YCICRLPYDvTRFMIECDACKDWFHGSCVGVEEEEAPDIDI----YHCPNC 47

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.

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gi 859821499  266 YCICRQPHNNRfMICCD--RCE-EWFHGDCVGISEArgrlleRNGEDYiCPNC 315
Cdd:cd15505     1 YCICNQVSYGE-MVACDnpNCPiEWFHFECVGLTAK------PKGKWY-CPEC 45

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.

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gi 859821499  281 CDRCEEWFHGDCVGISEargrLLERNGEDYICPNC 315
Cdd:cd15610    20 CDGCEEWFHLLCVGLSP----EEVAEDEDYICPSC 50

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

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gi 859821499  266 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEArgrllERNGEDYICPNC 315
Cdd:cd15522     1 ICpICKKPDDGSPMIGCDECDDWYHWECVGITDE-----PPEEDDWFCPKC 46