SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in developmental signalling and has also been proposed to be a phosphorylation binding module. It has been found mainly in two protein families: transcription factor S-II (TFIIS) and Spen (split end). The 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. The Spen protein family includes SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). They are characterized by containing RNA recognition motifs (RRMs) and a SPOC domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468 1053 IWKGFINMQSVAKFVTKAYPVSGCLDYLSEDLPDTIHIGGRIAPKTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1132
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 672048468 1133 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPVPSKLLPFEGPASNRNR 1183
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTR 131

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

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468    671 QNIRRSLKEILWKRVNDSDDLIMTENEVGKIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLREEISL 750
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 672048468    751 AKLVRMKPEELVSKELSMWTEK 772
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102

DNA polymerase III subunits gamma and tau; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 672048468  602 WPSATLSGTSARQAGPTPVIAASKKlPGSAAVVGIARKPMSANVPAASPVPGRLGPVSPAPSQPNS 667
Cdd:PRK14954  381 APSPAGSPDVKKKAPEPDLPQPDRH-PGPAKPEAPGARPAELPSPASAPTPEQQPPVARSAPLPPS 445

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 672048468 1053 IWKGFINMQSVAKFVTKAYPVSGCLDYLSEDLPDTIHIGGRIAPKTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1132
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 672048468 1133 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPVPSKLLPFEGPASNRNR 1183
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTR 131

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

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468    671 QNIRRSLKEILWKRVNDSDDLIMTENEVGKIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLREEISL 750
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 672048468    751 AKLVRMKPEELVSKELSMWTEK 772
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 672048468   666 NSQIRQNIRRSLKEILWKRVNDSDdlimtENEVGKIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLR 745
Cdd:pfam07500    2 GDKVRDKCRELLYDALAKDSTEAS-----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLS 76

                           90       100       110
                   ....*....|....*....|....*....|....
gi 672048468   746 EEISLAKLVRMKPEELVSKELSMWTEKPTKSVIE 779
Cdd:pfam07500   77 GEISPEKLVTMSPEEMASEELKKEREKIEKEALK 110

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

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 672048468    267 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEargrLLERNGEDYICPNC 316
Cdd:smart00249    1 YCsVCGKPDDGGELLQCDGCDRWYHQTCLGPPL----LEEEPDGKWYCPKC 47

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468  157 TLKELQNRLRRKREQEPVERSLRGIQNRLRKQRREEDPAEAGSVQigSIEEDTPRCKQEPEASQGPVSQSEKDdRENQLE 236
Cdd:COG5034    91 RAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYS--SAARRSSGEHRSAASSQGSRHTKLKK-RKNIHN 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468  237 GKATQ---GSKEESPREAGKP-----------------------KPECEVYDpNALYCICRQPHNNRfMICCD--RCE-E 287
Cdd:COG5034   168 LKRRSpelSSKREVSFTLESPsvpdtatrvkegnnggstksrgvSSEDNSEG-EELYCFCQQVSYGQ-MVACDnaNCKrE 245

                         170
                  ....*....|..
gi 672048468  288 WFHGDCVGISEA 299
Cdd:COG5034   246 WFHLECVGLKEP 257

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 672048468 1053 IWKGFINMQSVAKFVTKAYPVSGCLDYLSEDLPDTIHIGGRIAPKTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1132
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 672048468 1133 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPVPSKLLPFEGPASNRNR 1183
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTR 131

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 672048468 1053 IWKGFINMQSVAKFVTKAYPVSGCLDYLSEDLPDTIHIGGRIAPKTVWDYVGKLKSSVSKELCLIRFHPATEEEEVAYIS 1132
Cdd:cd21548     1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672048468 1133 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPVPSKLLPFEGPASNRNRSPGHLG 1189
Cdd:cd21548    81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLG 137

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 672048468 1053 IWKGFINMQSVAKFVTKAYPVSGCLDYLSED---LPDTIHIGGRIAPKTVWDYVGKLKSSVSKELCLIRFHPATE-EEEV 1128
Cdd:cd21538     1 VWSGKLTMPGVASFPASARQVGGPDLSSTWWtdlLPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDSsSDKA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672048468 1129 AYISLYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPVPSKLLPFEGPASNRNRSP 1185
Cdd:cd21538    81 AFDELFDYFVSRDRYGVVGPKGLAVKDLYLVPLPAGDPLPPFLLLLDDGPGPEPRDE 137

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

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468    671 QNIRRSLKEILWKRVNDSDDLIMTENEVGKIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLREEISL 750
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 672048468    751 AKLVRMKPEELVSKELSMWTEK 772
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 672048468  267 YCICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 316
Cdd:cd15552     1 YCICRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMEENIEEYVCPKC 50

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 672048468   666 NSQIRQNIRRSLKEILWKRVNDSDdlimtENEVGKIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLR 745
Cdd:pfam07500    2 GDKVRDKCRELLYDALAKDSTEAS-----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLS 76

                           90       100       110
                   ....*....|....*....|....*....|....
gi 672048468   746 EEISLAKLVRMKPEELVSKELSMWTEKPTKSVIE 779
Cdd:pfam07500   77 GEISPEKLVTMSPEEMASEELKKEREKIEKEALK 110

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        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 672048468  267 YCICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERngedYICPNC 316
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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 672048468  269 ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 316
Cdd:cd15638     4 FCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

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        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 672048468  267 YCICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERngedYICPNCTIL 319
Cdd:cd15640     1 YCVCRQPYDvNRFMIECDICKDWFHGSCVQVEEHHAADIDL----YHCPNCEVL 50

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 672048468   267 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLErngEDYICPNCT 317
Cdd:pfam00628    1 YCaVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPS---GEWLCPECK 49

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 672048468   628 PGSAAVVGIARKPM--SANVPAASPVPGRLGPVSPAPSQPNS------------QIRQNIRRSLKEILWKRVNDSDDLIM 693
Cdd:TIGR01385   83 PGGNPEDKTTVGESvnSVKQEAKSQSDKIEQPKYVSSSPRNAkndfvptavtndKVRDKCRELLYDALAKDSDHPPQSID 162

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468   694 TEnevgKIALHIEKEMFNLFQVTDNRYKSKYRSIMFNLKDPKNQGLFHRVLREEISLAKLVRMKPEELVSKELSMWTEKP 773
Cdd:TIGR01385  163 PE----AKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEI 238

                   ....*
gi 672048468   774 TKSVI 778
Cdd:TIGR01385  239 TKENL 243

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 672048468 1053 IWKGFINMQSV-AKFVTKAYPVSGCL--------DYLSEDLPDTIHIGGRIAPKTVWDYVGKLKSSvsKELCLIRFHP-A 1122
Cdd:cd21542     1 VWKGTLEYPEInAEFSGKIKFVGSSTklskqnvkEQQDALGDKKLEVEGRLSAETADKYLNQIMSS--RDLLVYELEPnE 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 672048468 1123 TEEEEVAYISLYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPVPsKLLPFEGPASNRNRS 1184
Cdd:cd21542    79 SSEDKTNFDKLFDYLHSRERYGVLKNKPSYVKDAYLIPLSAGDKPP-ILFIILNPISILEEE 139

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 672048468  267 YC-ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLlernGEDYICPNC 316
Cdd:cd15489     1 SCiVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSFVP----NGKWICPVC 48

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 672048468  267 YCICRQPHNNrFMICCDRCEEWFHGDCVGISeaRGRLleRNGEDYICPNC 316
Cdd:cd15518     1 YCFCRQGEGG-TMIECEICKEWYHVKCIKNG--RWKL--DDDDKFVCPIC 45

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
                  ....*....|....*....|....*....|....*..
gi 672048468  280 ICCDRCEEWFHGDCVGISEARGRLlernGEDYICPNC 316
Cdd:cd15517    17 VQCDGCDKWFHQFCLGLSNERYAD----EDKFKCPNC 49

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 672048468  267 YCICRQPHNNrFMICCDRCEEWFHGDCVGISEARGRLLERNGED-------YICPNC 316
Cdd:cd15606     1 YCICRKPFSG-FMLQCELCKDWFHSSCVPLPKSSSQKKGGNGSGqgakelkFLCPLC 56

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
                  ....*....|....*....|....*....|....*....|...
gi 672048468  275 NNRFMICCDRCEEWFHGDCVGISEARGRLLERngedYICPNCT 317
Cdd:cd15613    11 ADEFWICCDVCEKWYHGKCVKITPAKAEHIKQ----YKCPSCS 49

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 672048468  268 CICRQPHNN--RfMICCDRCEEWFHGDCVGISEArgrllERNGEDYICPNC 316
Cdd:cd15556     2 CSCGTRDDDgeR-MIACDVCEVWQHTRCVGIADN-----EEPPDHFLCRRC 46

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468  157 TLKELQNRLRRKREQEPVERSLRGIQNRLRKQRREEDPAEAGSVQigSIEEDTPRCKQEPEASQGPVSQSEKDdRENQLE 236
Cdd:COG5034    91 RAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYS--SAARRSSGEHRSAASSQGSRHTKLKK-RKNIHN 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672048468  237 GKATQ---GSKEESPREAGKP-----------------------KPECEVYDpNALYCICRQPHNNRfMICCD--RCE-E 287
Cdd:COG5034   168 LKRRSpelSSKREVSFTLESPsvpdtatrvkegnnggstksrgvSSEDNSEG-EELYCFCQQVSYGQ-MVACDnaNCKrE 245

                         170
                  ....*....|..
gi 672048468  288 WFHGDCVGISEA 299
Cdd:COG5034   246 WFHLECVGLKEP 257

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 672048468  268 CICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNC 316
Cdd:cd15570     2 CPCGSSMEDGSMIQCEGCKTWQHMDCVLIPDKPADGLPELPSKFYCELC 50

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 672048468  267 YCICRQPHNNrFMICCDRCEEWFHGDCVGI----SEARGRLLERNGEDYICPNC 316
Cdd:cd15516     1 ICLCGKALAA-GMLQCELCQDWFHGSCVAVprisSSPRPLAWWEGDRKFLCPLC 53

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 672048468 1053 IWKGFINMQSvaKFVTK--AYPVSGclDYLSED--LPDTIHIGGRiapkTVWDYVgKLKSSVSKELCLIrFHPATEEEEV 1128
Cdd:cd21546     1 KWSGTLAKSG--KPRCNvvAHPVSG--DVAREPvsLPEVLNVSHR----TDLEEV-AHKPVARAVLVLL-FAPENESDRG 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 672048468 1129 AYISLYSYFSSRGRFGVVA-NNNRHvkdLYLIPLSakDPVPSKLLPF 1174
Cdd:cd21546    71 AFDEFIDYLSSKDRAGVVKlPDNRT---LYLVPPS--EELFSQLLLN 112

PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 672048468  267 YCICRQPHNNRfMICCD--RCE-EWFHGDCVGIS-EARGRllerngedYICPNC 316
Cdd:cd15584     1 YCLCNQVSYGE-MIGCDndECPiEWFHFSCVGLThKPKGK--------WYCPKC 45

PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 672048468  268 CICRQPHNNRFMICCDRCEEWFHGDCVGISEargrllERNGEDYICPNCT 317
Cdd:cd15633     2 CICEMDEENGFMIQCEECLCWQHSVCMGLLE------ESIPEQYICYICR 45

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 672048468  280 ICCDRCEEWFHGDCvgisEARGRL-----LERNGEDYICPNC 316
Cdd:cd15615    20 VQCDSCSEWVHFEC----DGRTGLgafkyAKSDGLQYVCPRC 57

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 672048468  270 CRQPHNNR--FMICCDRCEEWFHGDCVGISEARGRllernGEDYICPNCT 317
Cdd:cd15686     8 CQRPCKDKvdWVQCDGGCDEWFHQVCVGVSPEMAE-----NEDYICINCA 52

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 672048468  270 CRQPHNNRF-MICCD-RCEEWFHGDCVGISearGRLLERngEDYICPNC 316
Cdd:cd15687     7 CLQPEGEEVdWVQCDgSCNRWFHQVCVGVS---AEMAEK--EDYICVSC 50

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 672048468  268 CICRQPHNNRFMICCDRCEEWFHGDCVGISEArgrlleRNGEDYICPNC 316
Cdd:cd15632     4 CFCMKPFAGRPMIECNECHTWIHLSCAKIRKS------NVPEVYVCQKC 46

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 672048468  268 CICRQPHNNRFMICCDRCEEWFHGDCVgiseaRGRLLERNGEDYICPNC 316
Cdd:cd15543     3 RKCGLSDHPEWILLCDRCDAGYHTACL-----RPPLMIIPDGNWFCPPC 46

DNA polymerase III subunits gamma and tau; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 672048468  602 WPSATLSGTSARQAGPTPVIAASKKlPGSAAVVGIARKPMSANVPAASPVPGRLGPVSPAPSQPNS 667
Cdd:PRK14954  381 APSPAGSPDVKKKAPEPDLPQPDRH-PGPAKPEAPGARPAELPSPASAPTPEQQPPVARSAPLPPS 445

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 672048468  267 YC-ICRQPHNnrfMICCDRCEEWFHGDCVGIseargRLLERNGEDYICPNC 316
Cdd:cd15532     1 FCrVCKDGGE---LLCCDGCPSSYHLHCLNP-----PLAEIPDGDWFCPRC 43