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Conserved domains on  [gi|124487309|ref|NP_001074549|]
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PHD finger protein 3 isoform 1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
SPOC_PHF3 cd21548
SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3); PHF3 ...
1187-1327 2.51e-99

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.


:

Pssm-ID: 439211  Cd Length: 141  Bit Score: 315.27  E-value: 2.51e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21548     1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487309 1267 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1327
Cdd:cd21548    81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLIIR 141
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
904-1017 8.08e-38

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.


:

Pssm-ID: 462184  Cd Length: 112  Bit Score: 138.11  E-value: 8.08e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   904 DQIRQSVRHSLKDILMKRLTDSNlkipEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 983
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78
                           90       100       110
                   ....*....|....*....|....*....|....
gi 124487309   984 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 1017
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
697-747 3.17e-34

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.


:

Pssm-ID: 277108  Cd Length: 51  Bit Score: 125.42  E-value: 3.17e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124487309  697 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 747
Cdd:cd15638     1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51
SF-CC1 super family cl36939
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1916-2025 9.91e-08

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.


The actual alignment was detected with superfamily member TIGR01622:

Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 56.85  E-value: 9.91e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1916 RERH-----DKDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDgKSADKKPDRPKgedh 1990
Cdd:TIGR01622    7 RERLrdsssAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRY-RPREKRRRRGD---- 81
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 124487309  1991 EKEKERDKSKHKEgEKDRERYHKDRDHTDRVKSKR 2025
Cdd:TIGR01622   82 SYRRRRDDRRSRR-EKPRARDGTPEPLTEDERDRR 115
PHA03369 super family cl25753
capsid maturational protease; Provisional
983-1184 1.94e-04

capsid maturational protease; Provisional


The actual alignment was detected with superfamily member PHA03369:

Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 46.53  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  983 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEI--EIESDAPMKEQEA 1051
Cdd:PHA03369  444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIkkIAESEFKNAGAKT 523
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1052 AIEIQEPSANKSMEKPDvsekQKEEVDSTSKDTTSQHRQhlfdlncKICIGRMAPPIDDLSPKTVKVVVGGARkhSDNEA 1131
Cdd:PHA03369  524 AAANIEPNCSADAAAPA----TKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124487309 1132 ESLADALSSTTNILTSDL--FEEEKQESP--KSTFSPTPRPEMPGTVEVESTFLARL 1184
Cdd:PHA03369  591 EALAGAIETLLTQASAQPagLSLPAPAVPvnASTPASTPPPLAPQEPPQPGTSAPSL 647
 
Name Accession Description Interval E-value
SPOC_PHF3 cd21548
SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3); PHF3 ...
1187-1327 2.51e-99

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.


Pssm-ID: 439211  Cd Length: 141  Bit Score: 315.27  E-value: 2.51e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21548     1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487309 1267 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1327
Cdd:cd21548    81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLIIR 141
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
1180-1328 1.29e-44

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 158.67  E-value: 1.29e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1180 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 1259
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487309  1260 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAadkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 1328
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVIHAKSADVKDLYLFPPCE---FLELLLPV-GLSLEVSEPNLLLGVVVRK 142
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
904-1017 8.08e-38

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.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 138.11  E-value: 8.08e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   904 DQIRQSVRHSLKDILMKRLTDSNlkipEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 983
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78
                           90       100       110
                   ....*....|....*....|....*....|....
gi 124487309   984 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 1017
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
908-1008 7.17e-37

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


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 134.75  E-value: 7.17e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309    908 QSVRHSLKDILMKRLTDSNLKIPEE-KAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 986
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80
                            90       100
                    ....*....|....*....|..
gi 124487309    987 DHLIRMSPEELASKELAAWRRR 1008
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
697-747 3.17e-34

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.


Pssm-ID: 277108  Cd Length: 51  Bit Score: 125.42  E-value: 3.17e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124487309  697 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 747
Cdd:cd15638     1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
827-1030 1.16e-16

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.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 82.96  E-value: 1.16e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   827 IKKWQLAPLRKLSQPHLPRrsseekseKIAKESTALASTGERVARSGTHEKQETKKKKmeKGGPNVHPPAATSKP-SADQ 905
Cdd:TIGR01385   68 IKSWKKVVDKNKSDHPGGN--------PEDKTTVGESVNSVKQEAKSQSDKIEQPKYV--SSSPRNAKNDFVPTAvTNDK 137
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   906 IRQSVRHSLKDILMKRLTDS-NLKIPEEKAAKvatkIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEV 984
Cdd:TIGR01385  138 VRDKCRELLYDALAKDSDHPpQSIDPEAKAIQ----IEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEI 213
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 124487309   985 TPDHLIRMSPEELASKELaawRRRENRHTIEMIEKEQREVERRPIT 1030
Cdd:TIGR01385  214 TPEKLATMTAEEMASAEL---KQEREEITKENLFEAQGAKIQKAVT 256
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
698-747 2.53e-13

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.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 65.98  E-value: 2.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 124487309   698 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeeDKEYVCVRC 747
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIP---SGEWLCPEC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
698-747 8.28e-13

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.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 64.54  E-value: 8.28e-13
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 124487309    698 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCVRC 747
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLL----EEEPDGKWYCPKC 47
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1916-2025 9.91e-08

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.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 56.85  E-value: 9.91e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1916 RERH-----DKDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDgKSADKKPDRPKgedh 1990
Cdd:TIGR01622    7 RERLrdsssAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRY-RPREKRRRRGD---- 81
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 124487309  1991 EKEKERDKSKHKEgEKDRERYHKDRDHTDRVKSKR 2025
Cdd:TIGR01622   82 SYRRRRDDRRSRR-EKPRARDGTPEPLTEDERDRR 115
PHA03369 PHA03369
capsid maturational protease; Provisional
983-1184 1.94e-04

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 46.53  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  983 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEI--EIESDAPMKEQEA 1051
Cdd:PHA03369  444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIkkIAESEFKNAGAKT 523
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1052 AIEIQEPSANKSMEKPDvsekQKEEVDSTSKDTTSQHRQhlfdlncKICIGRMAPPIDDLSPKTVKVVVGGARkhSDNEA 1131
Cdd:PHA03369  524 AAANIEPNCSADAAAPA----TKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124487309 1132 ESLADALSSTTNILTSDL--FEEEKQESP--KSTFSPTPRPEMPGTVEVESTFLARL 1184
Cdd:PHA03369  591 EALAGAIETLLTQASAQPagLSLPAPAVPvnASTPASTPPPLAPQEPPQPGTSAPSL 647
PRK12678 PRK12678
transcription termination factor Rho; Provisional
1873-2020 2.56e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.97  E-value: 2.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1873 DIRRPERRHSDPWGRQDQQQPDRpfnRGKGDRQRfysdshhlKRERHDKDWEQESERHRHRDRSQERDRDRKSKEEAAAH 1952
Cdd:PRK12678  108 ARAAAAAAAEAASAPEAAQARER---RERGEAAR--------RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRG 176
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487309 1953 KDKERPRLSH-GDRAPDGKASRDGKSADKKPDRPKGEDHEKEKERDKSKHKEGEKDRERYHKDRDHTDR 2020
Cdd:PRK12678  177 DREDRQAEAErGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRE 245
 
Name Accession Description Interval E-value
SPOC_PHF3 cd21548
SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3); PHF3 ...
1187-1327 2.51e-99

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.


Pssm-ID: 439211  Cd Length: 141  Bit Score: 315.27  E-value: 2.51e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21548     1 IWKGFINMPSVAKFVTKAYPVSGSLEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFSPVTEEDQISYTL 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487309 1267 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1327
Cdd:cd21548    81 LYAYFSSRKRYGVVANNMKQVKDMYLIPLGASEKIPHHLVPFDGPGLELHRPNLLLGLIIR 141
SPOC_PHF3-like cd21541
SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3), ...
1187-1327 3.20e-82

SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3), death-inducer obliterator (Dido) variants, and similar proteins; 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. This group also includes the protein products of the Dido gene that encodes three alternative splicing variants (Dido1, 2, and 3), which have been implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. The Dido gene is a bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. 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). 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. This model corresponds to the SPOC domain of the PHF3-like group; the SPOC domain is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439204  Cd Length: 141  Bit Score: 266.02  E-value: 3.20e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21541     1 VWKGFISMQEVAKFVASAYHVSGPCEDLSEDLPDTLEVCGRISPEQVWDYLSKLKQSGTKEIIVIRFHPANEEEKVSYIS 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487309 1267 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1327
Cdd:cd21541    81 LYSYLSSRKRCGVVGNNSKHVKDMYLIPLASHQPIPQVLLPFDGPGLEETRPHMLLGIIVR 141
SPOC_DIDO1-like cd21547
SPOC (Spen paralog and ortholog C-terminal) domain found in some death-inducer obliterator ...
1187-1329 3.55e-76

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.


Pssm-ID: 439210  Cd Length: 143  Bit Score: 249.08  E-value: 3.55e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21547     1 IWKGFINMQSVAKFVTKAYPVSGSFDYLSEDLPDTIHIGGRISPKTVWDYVGKLKSSLSKELCLIRFHPATEEEEVAYIS 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124487309 1267 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIRQK 1329
Cdd:cd21547    81 LYSYFSSRGRFGVVANNNRHVKDLYLIPLSAKDPIPSKLLPFEGPGLESTRPNIILGLVICQK 143
SPOC_PPS-like cd22581
SPOC (Spen paralog and ortholog C-terminal) domain found in Drosophila melanogaster protein ...
1187-1327 5.49e-54

SPOC (Spen paralog and ortholog C-terminal) domain found in Drosophila melanogaster protein partner of Sans-fille and similar proteins; Drosophila melanogaster protein partner of Sans-fille (PPS), also called protein partner of Snf, is a homolog of human DIDO. It mediates diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing. PPS associates with spliceosomal RNAs including the U1 snRNP protein Sans-fille (Snf) to mediate sex determination gene Sex-lethal (Sxl) splicing autoregulation. Alternative splicing of the Sxl pre-mRNA determines gender during development in Drosophila, producing protein-encoding mRNAs in females but yielding inactive and truncated mRNAs in males. PPS contains a plant homeodomain (PHD) finger, Brahma and Kismet (BRK), a transcription elongation factor S-II subunit M (TFSIIM) domain, and a 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.


Pssm-ID: 439214  Cd Length: 142  Bit Score: 185.50  E-value: 5.49e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd22581     1 VWKGTINMPDVAKFNVSAQVVSGNSDDLSLDLPKVLDVVGRIAPETVWDYIGKLKKSPTKEIVVVRLTPASEEDEMSYNT 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124487309 1267 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGL-ELHRPNLLLGLIIR 1327
Cdd:cd22581    81 FFEYLSSRNRLGVIGSVSKAIKDFYILPLPKESPIPEVLLPLDGPGLfENRRPNLLLGIIVR 142
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
1180-1328 1.29e-44

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 158.67  E-value: 1.29e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1180 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 1259
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487309  1260 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAadkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 1328
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVIHAKSADVKDLYLFPPCE---FLELLLPV-GLSLEVSEPNLLLGVVVRK 142
SPOC_TFIIS cd21538
SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II ...
1187-1327 4.10e-42

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.


Pssm-ID: 439201  Cd Length: 146  Bit Score: 151.65  E-value: 4.10e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSG---SPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTE-EDQI 1262
Cdd:cd21538     1 VWSGKLTMPGVASFPASARQVGGpdlSSTWWTDLLPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDSsSDKA 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124487309 1263 SYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRP-NLLLGLIIR 1327
Cdd:cd21538    81 AFDELFDYFVSRDRYGVVGPKGLAVKDLYLVPLPAGDPLPPFLLLLDDGPGPEPRDeDLLLGVIVL 146
SPOC_SPOCD1 cd21540
SPOC (Spen paralog and ortholog C-terminal) domain found in SPOC domain-containing protein 1 ...
1187-1326 8.82e-41

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.


Pssm-ID: 439203  Cd Length: 138  Bit Score: 147.58  E-value: 8.82e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21540     1 LWEGAIQMFSIKQFGAKAYLVSGHSSQLIQALPAVIRSRGCILPESVWDYLDSIWPAEAKEMCLVRFAPAGARDSQNYRM 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487309 1267 LFAYFSSRKRYG-VAANNMkqvkDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLII 1326
Cdd:cd21540    81 LYSYLNNKQRYGiVDSEKM----DMFLIPLPAFQPVPAKLRPLGGPGLEATHSSLLLALIL 137
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
904-1017 8.08e-38

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.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 138.11  E-value: 8.08e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   904 DQIRQSVRHSLKDILMKRLTDSNlkipEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 983
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78
                           90       100       110
                   ....*....|....*....|....*....|....
gi 124487309   984 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 1017
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
908-1008 7.17e-37

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


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 134.75  E-value: 7.17e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309    908 QSVRHSLKDILMKRLTDSNLKIPEE-KAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 986
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80
                            90       100
                    ....*....|....*....|..
gi 124487309    987 DHLIRMSPEELASKELAAWRRR 1008
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102
PHD_PHF3 cd15638
PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein ...
697-747 3.17e-34

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.


Pssm-ID: 277108  Cd Length: 51  Bit Score: 125.42  E-value: 3.17e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124487309  697 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 747
Cdd:cd15638     1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
697-747 5.26e-26

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.


Pssm-ID: 277027  Cd Length: 50  Bit Score: 102.09  E-value: 5.26e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124487309  697 QCGfCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 747
Cdd:cd15552     1 YCI-CRKPHNNRFMICCDRCEEWFHGDCVGITEAQGKEMEENIEEYVCPKC 50
SPOC_SF cd21520
SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in ...
1187-1326 5.38e-18

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.


Pssm-ID: 439200  Cd Length: 138  Bit Score: 82.33  E-value: 5.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1266
Cdd:cd21520     1 VWQGLLALKNDPTAAARLHFVSGNNVLALSELPPVLRIAQRMRLNATQLEGVARRMAVATDYCLVLALPCGRDDESLKAA 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487309 1267 LFAYFSSRKRYGVAANnmkQVKDMYLIPLGAADKIPHPLVPF-DGPGLELHRPNLLLGLII 1326
Cdd:cd21520    81 FITYLQAKQRAGIASN---QPAYVLQLFPPCEFSESHLSRLApDLLASIVTISPHLMIVIL 138
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
827-1030 1.16e-16

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.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 82.96  E-value: 1.16e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   827 IKKWQLAPLRKLSQPHLPRrsseekseKIAKESTALASTGERVARSGTHEKQETKKKKmeKGGPNVHPPAATSKP-SADQ 905
Cdd:TIGR01385   68 IKSWKKVVDKNKSDHPGGN--------PEDKTTVGESVNSVKQEAKSQSDKIEQPKYV--SSSPRNAKNDFVPTAvTNDK 137
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309   906 IRQSVRHSLKDILMKRLTDS-NLKIPEEKAAKvatkIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEV 984
Cdd:TIGR01385  138 VRDKCRELLYDALAKDSDHPpQSIDPEAKAIQ----IEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEI 213
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 124487309   985 TPDHLIRMSPEELASKELaawRRRENRHTIEMIEKEQREVERRPIT 1030
Cdd:TIGR01385  214 TPEKLATMTAEEMASAEL---KQEREEITKENLFEAQGAKIQKAVT 256
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
701-747 5.26e-15

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.


Pssm-ID: 277035  Cd Length: 47  Bit Score: 70.84  E-value: 5.26e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124487309  701 CKKPH-GNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 747
Cdd:cd15560     4 CRTPYdESQFYIGCDRCQDWFHGRCVGILQSEAEKI----DEYVCPQC 47
PHD_DIDO1_like cd15639
PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family ...
694-747 5.31e-15

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.


Pssm-ID: 277109  Cd Length: 54  Bit Score: 70.76  E-value: 5.31e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 124487309  694 PSKQCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 747
Cdd:cd15639     1 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLERNGEDYICPNC 54
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
698-747 2.53e-13

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.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 65.98  E-value: 2.53e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 124487309   698 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeeDKEYVCVRC 747
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIP---SGEWLCPEC 48
SPOC_Bye1p-like cd21542
SPOC (Spen paralog and ortholog C-terminal) domain found in Saccharomyces cerevisiae bypass of ...
1187-1302 3.25e-13

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.


Pssm-ID: 439205  Cd Length: 153  Bit Score: 69.24  E-value: 3.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSV-AKFVTKAYPVSGS--------PEYLTEDLPDSIQVGGRISPQTVWDYVEKIKAsgTKEICVVRFTPVT 1257
Cdd:cd21542     1 VWKGTLEYPEInAEFSGKIKFVGSStklskqnvKEQQDALGDKKLEVEGRLSAETADKYLNQIMS--SRDLLVYELEPNE 78
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 124487309 1258 E-EDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIP 1302
Cdd:cd21542    79 SsEDKTNFDKLFDYLHSRERYGVLKNKPSYVKDAYLIPLSAGDKPP 124
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
698-747 8.28e-13

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.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 64.54  E-value: 8.28e-13
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 124487309    698 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCVRC 747
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLL----EEEPDGKWYCPKC 47
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
701-747 1.85e-11

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.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 60.47  E-value: 1.85e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 124487309  701 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 747
Cdd:cd15553     4 CRSSDISRFMIGCDNCEEWYHGDCINITEKEAKAI----KEWYCQQC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
698-747 1.82e-10

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.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 57.71  E-value: 1.82e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124487309  698 CGFCKKPH-GNRFMVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCVRC 747
Cdd:cd15489     2 CIVCGKGGdLGGELLQCDGCGKWFHADCLGPPLS----SFVPNGKWICPVC 48
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
701-747 4.67e-10

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.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 56.62  E-value: 4.67e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124487309  701 CKKP-HGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 747
Cdd:cd15554     4 CRQPyDVTRFMIECDVCKDWFHGSCVGVEEHQANDI----ERYHCPNC 47
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
701-747 3.61e-09

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.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 54.02  E-value: 3.61e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 124487309  701 CKKPHGNRFMVGCGRCDDWFHGDCVglslsqaqQMGEEDKE----YVCVRC 747
Cdd:cd16039     4 CQKPDDGRWMIACDGCDEWYHFTCV--------NIPEADVElvdsFFCPPC 46
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
701-747 1.53e-08

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.


Pssm-ID: 277083 [Multi-domain]  Cd Length: 50  Bit Score: 52.33  E-value: 1.53e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124487309  701 CKKPHGNRF-MVGCGRCDDWFHGDCVGLSLSQAqqmgEEDKEYVCVRC 747
Cdd:cd15610     7 CLKPTGDEVnWVQCDGCEEWFHLLCVGLSPEEV----AEDEDYICPSC 50
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1916-2025 9.91e-08

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.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 56.85  E-value: 9.91e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1916 RERH-----DKDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDgKSADKKPDRPKgedh 1990
Cdd:TIGR01622    7 RERLrdsssAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRY-RPREKRRRRGD---- 81
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 124487309  1991 EKEKERDKSKHKEgEKDRERYHKDRDHTDRVKSKR 2025
Cdd:TIGR01622   82 SYRRRRDDRRSRR-EKPRARDGTPEPLTEDERDRR 115
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
698-747 1.00e-07

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).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 49.98  E-value: 1.00e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 124487309  698 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQaqqmgEEDKEYVCVRC 747
Cdd:cd15522     2 CPICKKPDDGSPMIGCDECDDWYHWECVGITDEP-----PEEDDWFCPKC 46
PHD_AL_plant cd15613
PHD finger found in plant Alfin1-like (AL) proteins; AL proteins are ubiquitously expressed ...
697-749 3.15e-07

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.


Pssm-ID: 277085  Cd Length: 51  Bit Score: 48.65  E-value: 3.15e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 124487309  697 QCGFCKKPHGN-RFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRCCA 749
Cdd:cd15613     1 QCGSCGGNYTAdEFWICCDVCEKWYHGKCVKITPAKAEHI----KQYKCPSCSN 50
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1928-2010 3.76e-07

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.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 54.93  E-value: 3.76e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1928 ERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRD---GKSADKKPDRPKGEDHEKEKERDKSKHKEG 2004
Cdd:TIGR01622    6 ERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDyyrGRERRSRSRRPNRRYRPREKRRRRGDSYRR 85

                   ....*.
gi 124487309  2005 EKDRER 2010
Cdd:TIGR01622   86 RRDDRR 91
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
1915-2015 5.71e-07

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.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 54.51  E-value: 5.71e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1915 KRERHDKDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDG------KASRDGKSADKKPdRPKGE 1988
Cdd:TIGR01642   11 KSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSlryssvRRSRDRPRRRSRS-VRSIE 89
                           90       100
                   ....*....|....*....|....*..
gi 124487309  1989 DHEKEKERDKSKHKEGEKDRERYHKDR 2015
Cdd:TIGR01642   90 QHRRRLRDRSPSNQWRKDDKKRSLWDI 116
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
701-747 7.05e-07

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.


Pssm-ID: 277079  Cd Length: 56  Bit Score: 47.82  E-value: 7.05e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 124487309  701 CKKPHGNrFMVGCGRCDDWFHGDCVGLSLSQAQQ-------MGEEDKEYVCVRC 747
Cdd:cd15606     4 CRKPFSG-FMLQCELCKDWFHSSCVPLPKSSSQKkggngsgQGAKELKFLCPLC 56
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
701-747 1.24e-06

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.


Pssm-ID: 277110  Cd Length: 50  Bit Score: 46.90  E-value: 1.24e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124487309  701 CKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 747
Cdd:cd15640     4 CRQPYDvNRFMIECDICKDWFHGSCVQVEEHHAADI----DLYHCPNC 47
PHD_UBR7 cd15542
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ...
701-747 5.36e-06

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.


Pssm-ID: 277017  Cd Length: 54  Bit Score: 45.44  E-value: 5.36e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 124487309  701 CKKPH------GNRFMVGCGRCDDWFHGDCVGLSLSQAQqmGEEDKEYVCVRC 747
Cdd:cd15542     4 CDRPYpdpedeVEDEMIQCVLCEDWFHGRHLGLTPPEPD--PDEFDEMICSGC 54
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
698-747 5.91e-06

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.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 45.00  E-value: 5.91e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 124487309  698 CGFckkPHGNRFMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDkeYVCVRC 747
Cdd:cd15550     4 CGF---EHDDGFMICCDKCSVWQHGDCMGID----RENIPDS--YLCEQC 44
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
697-747 5.93e-06

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).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 45.23  E-value: 5.93e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 124487309  697 QCGFCKKPHGNR--FMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDKEYVCVRC 747
Cdd:cd15517     1 VCGICNLETAAVdeLWVQCDGCDKWFHQFCLGLS----NERYADEDKFKCPNC 49
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1886-1998 3.34e-05

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.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 48.76  E-value: 3.34e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1886 GRQDQQQPDRPFNRGKGDRQRFYSDSHHLKRER-HDKDWEQESERHRHRDRSQERDRDRKSKEEAAahKDKERPRLSHGD 1964
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRsRDRERSRSRRRDRHRDRDYYRGRERRSRSRRP--NRRYRPREKRRR 78
                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 124487309  1965 RAPDGKASRDGKSADKKPDRPKGE--DHEKEKERDK 1998
Cdd:TIGR01622   79 RGDSYRRRRDDRRSRREKPRARDGtpEPLTEDERDR 114
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
701-747 7.83e-05

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.


Pssm-ID: 277045  Cd Length: 50  Bit Score: 42.06  E-value: 7.83e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 124487309  701 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCVRC 747
Cdd:cd15570     4 CGSSMEDGSMIQCEGCKTWQHMDCVLIPDKPADGLPELPSKFYCELC 50
PHD3_KDM5B cd15687
PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis ...
701-747 8.34e-05

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.


Pssm-ID: 277157  Cd Length: 50  Bit Score: 41.86  E-value: 8.34e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 124487309  701 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVRC 747
Cdd:cd15687     7 CLQPEGEEVdWVQCdGSCNRWFHQVCVGVSAEMA-----EKEDYICVSC 50
SPOC_FPA-like cd21546
SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering ...
1187-1296 1.15e-04

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.


Pssm-ID: 439209  Cd Length: 125  Bit Score: 43.82  E-value: 1.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1187 IWKGFINMPSvaKFVTK--AYPVSGSPEYLTEDLPDSIQVGGRispqTVWDYVEKIKASGtkEICVVRFTPVTEEDQISY 1264
Cdd:cd21546     1 KWSGTLAKSG--KPRCNvvAHPVSGDVAREPVSLPEVLNVSHR----TDLEEVAHKPVAR--AVLVLLFAPENESDRGAF 72
                          90       100       110
                  ....*....|....*....|....*....|..
gi 124487309 1265 TLLFAYFSSRKRYGVAanNMKQVKDMYLIPLG 1296
Cdd:cd21546    73 DEFIDYLSSKDRAGVV--KLPDNRTLYLVPPS 102
PHD_PHF8 cd15642
PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, ...
700-735 1.50e-04

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.


Pssm-ID: 277112  Cd Length: 52  Bit Score: 41.16  E-value: 1.50e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 124487309  700 FCKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQAQQM 735
Cdd:cd15642     4 LCRLPYDvTRFMIECDVCQDWFHGSCVGVEEEKAAEI 40
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
710-747 1.59e-04

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 41.28  E-value: 1.59e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 124487309  710 MVGCGRCDDWFHGDCVGLSLSQAQQMGE--EDKEYVCVRC 747
Cdd:cd15508    18 MMQCSQCDHWVHAKCEGLSDEMYEILSYlpESIEYTCSLC 57
PHA03369 PHA03369
capsid maturational protease; Provisional
983-1184 1.94e-04

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 46.53  E-value: 1.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  983 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEI--EIESDAPMKEQEA 1051
Cdd:PHA03369  444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIkkIAESEFKNAGAKT 523
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1052 AIEIQEPSANKSMEKPDvsekQKEEVDSTSKDTTSQHRQhlfdlncKICIGRMAPPIDDLSPKTVKVVVGGARkhSDNEA 1131
Cdd:PHA03369  524 AAANIEPNCSADAAAPA----TKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124487309 1132 ESLADALSSTTNILTSDL--FEEEKQESP--KSTFSPTPRPEMPGTVEVESTFLARL 1184
Cdd:PHA03369  591 EALAGAIETLLTQASAQPagLSLPAPAVPvnASTPASTPPPLAPQEPPQPGTSAPSL 647
PHD_PHF13 cd15632
PHD finger found in PHD finger protein 13 (PHF13); PHF13, also termed survival time-associated ...
700-747 2.02e-04

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.


Pssm-ID: 277102  Cd Length: 47  Bit Score: 40.79  E-value: 2.02e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124487309  700 FCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMgeedkeYVCVRC 747
Cdd:cd15632     5 FCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEV------YVCQKC 46
PHD_PHF2 cd15641
PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger ...
701-732 4.94e-04

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).


Pssm-ID: 277111  Cd Length: 50  Bit Score: 39.62  E-value: 4.94e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 124487309  701 CKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQA 732
Cdd:cd15641     4 CRLPYDvTRFMIECDACKDWFHGSCVGVEEEEA 36
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
700-747 5.61e-04

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.


Pssm-ID: 276993  Cd Length: 45  Bit Score: 39.25  E-value: 5.61e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124487309  700 FCKKPHGNrFMVGCGRCDDWFHGDCVGlslsQAQQMGEEDKEYVCVRC 747
Cdd:cd15518     3 FCRQGEGG-TMIECEICKEWYHVKCIK----NGRWKLDDDDKFVCPIC 45
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
1929-2025 9.67e-04

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.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 44.14  E-value: 9.67e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1929 RHRHRDRSQERDRDRkskeeaAAHKDKERPRLSHGDRapDGKASRDgKSADKKPDRPKGEDHEKEKERDKSKHKEGEKDR 2008
Cdd:TIGR01622    1 RYRDRERERLRDSSS------AGDRDRRRDKGRERSR--DRSRDRE-RSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYR 71
                           90
                   ....*....|....*..
gi 124487309  2009 ERyHKDRDHTDRVKSKR 2025
Cdd:TIGR01622   72 PR-EKRRRRGDSYRRRR 87
PHD3_Lid2p_like cd15520
PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
710-747 2.14e-03

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


Pssm-ID: 276995  Cd Length: 47  Bit Score: 37.97  E-value: 2.14e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 124487309  710 MVGCGRCDDWFHGDCVGLSLSQAQQMgeedKEYVCVRC 747
Cdd:cd15520    14 MIFCDRCERTVHLDCVGLSDRIVDSP----SEFFCPEC 47
PHD3_KDM5A cd15686
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone ...
701-747 2.29e-03

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.


Pssm-ID: 277156  Cd Length: 52  Bit Score: 38.13  E-value: 2.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 124487309  701 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCVRC 747
Cdd:cd15686     8 CQRPCKDKVdWVQCdGGCDEWFHQVCVGVSPEMA-----ENEDYICINC 51
PRK12678 PRK12678
transcription termination factor Rho; Provisional
1873-2020 2.56e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 42.97  E-value: 2.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309 1873 DIRRPERRHSDPWGRQDQQQPDRpfnRGKGDRQRfysdshhlKRERHDKDWEQESERHRHRDRSQERDRDRKSKEEAAAH 1952
Cdd:PRK12678  108 ARAAAAAAAEAASAPEAAQARER---RERGEAAR--------RGAARKAGEGGEQPATEARADAAERTEEEERDERRRRG 176
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487309 1953 KDKERPRLSH-GDRAPDGKASRDGKSADKKPDRPKGEDHEKEKERDKSKHKEGEKDRERYHKDRDHTDR 2020
Cdd:PRK12678  177 DREDRQAEAErGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRE 245
PHD2_KDM5A_like cd15516
PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar ...
709-747 2.81e-03

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.


Pssm-ID: 276991  Cd Length: 53  Bit Score: 37.68  E-value: 2.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 124487309  709 FMVGCGRCDDWFHGDCVGLSLSQAQQMG----EEDKEYVCVRC 747
Cdd:cd15516    11 GMLQCELCQDWFHGSCVAVPRISSSPRPlawwEGDRKFLCPLC 53
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
1921-2015 7.50e-03

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.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.03  E-value: 7.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487309  1921 KDWEQESERHRHRDRSQERDRDRKSKEEAAAHKDKERPRLSHGDRAPDGKASRDGKSADKKpDRPKGEDHEKEKERDKSK 2000
Cdd:TIGR01642    1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSR-SPRSLRYSSVRRSRDRPR 79
                           90
                   ....*....|....*
gi 124487309  2001 HKEGEKDRERYHKDR 2015
Cdd:TIGR01642   80 RRSRSVRSIEQHRRR 94
PHD_PYGO cd15551
PHD finger found in PYGO proteins; The family includes Drosophila melanogaster protein pygopus ...
697-747 9.85e-03

PHD finger found in PYGO proteins; The family includes Drosophila melanogaster protein pygopus (dPYGO) and its two homologs, PYGO1 and PYGO2. dPYGO is a fundamental Wnt signaling transcriptional component in Drosophila. PYGO1 is essential for the association with Legless (Lgs)/Bcl9 that acts an adaptor between Pygopus (Pygo) and Arm/beta-catenin. dPYGO and PYGO2 function as context-dependent beta-catenin coactivators, and they bind di- and trimethylated lysine 4 of histone H3 (H3K4me2/3). Moreover, PYGO2 acts as a histone methylation reader, and a chromatin remodeler in a testis-specific and Wnt-unrelated manner. It also mediates chromatin regulation and links Wnt signaling and Notch signaling to suppress the luminal/alveolar differentiation competence of mammary stem and basal cells. PYGO2 also plays a new role in rRNA transcription during cancer cell growth. It regulates mammary tumor initiation and heterogeneity in MMTV-Wnt1 mice. All family members contain a plant homeodomain (PHD) finger.


Pssm-ID: 277026  Cd Length: 54  Bit Score: 36.19  E-value: 9.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 124487309  697 QCGFCKKP-HGNRFMVGC-GRCDDWFHGDCVGLSLSQAQQ-MGEEDKEYVCVRC 747
Cdd:cd15551     1 PCGICNNEvNDDDDAILCeSSCNKWFHRTCTGLTESAYDLlTSEESAEWVCDSC 54
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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