The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain; Has a putative AT-hook	(PMID: 10575013) obtained a motif by SELEX and showed that mutating the sequence diminished binding in vitro. Unusual for a PHD/Ring finger, but its there in the literature.

Description

Description:

bromodomain PHD finger transcription factor [Source:HGNC Symbol;Acc:HGNC:3581]

Entrez Summary

Ensembl ID:

ENSG00000171634

External Link:

CisBP

Interpro

IPR001487; IPR001965; IPR004022; IPR011011; IPR018359; IPR018500; IPR018501; IPR019786; IPR019787; IPR028942;

Protein Domain:

ENSP00000307208

Protein Domain:

ENSP00000343837

Protein Domain:

ENSP00000388405

Protein Domain:

ENSP00000462535

Protein Domain:

ENSP00000463845

Protein Domain:

ENSP00000463736

Protein Domain:

ENSP00000443949

Protein Domain:

ENSP00000462703

Domain:

Protein: ENSP00000307208	DBD: Other	Other: Bromodomain, DDT, PHD, WHIM1, WSD
Protein: ENSP00000343837	DBD: Other	Other: Bromodomain, PHD
Protein: ENSP00000388405	DBD: Other	Other: Bromodomain, DDT, PHD, WHIM1, WSD
Protein: ENSP00000462535	DBD: Other	Other:
Protein: ENSP00000463845	DBD: Other	Other: Bromodomain, DUF4428, PHD
Protein: ENSP00000463736	DBD: Other	Other: Bromodomain
Protein: ENSP00000443949	DBD: Other	Other:
Protein: ENSP00000462703	DBD: Other	Other: Bromodomain

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_Transcription Factor Binding tf co-factor binding DNA-Binding sequence-specific_DNA Binding_ PMIDS:10575013 10727212
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	No
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	No
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	No
GO-Info
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	2a1, Lower confidence direct evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

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Bromodomains can interact specifically with acetylated lysine [3].", "database": "PfamA", "aliStart": 2810, "scoreName": "E-value", "accession": "PF00439.23", "start": 2810, "score": 2.1999999999999997e-25, "identifier": "Bromodomain", "type": "DBD", "aliEnd": 2892}}, {"startStyle": "straight", "end": 437, "endStyle": "straight", "aliStart": 393, "text": "PHD", "colour": "#9999ff", "aliEnd": 435, "start": 392, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 437, "description": "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 [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 393, "scoreName": "E-value", "accession": "PF00628.27", "start": 392, "score": 2.1e-18, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 435}}, {"startStyle": "straight", "end": 2792, "endStyle": "straight", "aliStart": 2743, "text": "PHD", "colour": "#9999ff", "aliEnd": 2791, "start": 2743, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 2792, "description": "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 [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 2743, "scoreName": "E-value", "accession": "PF00628.27", "start": 2743, "score": 2.1e-18, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 2791}}, {"startStyle": "straight", "end": 297, "endStyle": "straight", "aliStart": 241, "text": "DDT", "colour": "#9999ff", "aliEnd": 297, "start": 241, "href": "http://pfam.xfam.org/family/PF02791.15", "type": "pfama", "display": "true", "metadata": {"end": 297, "description": "The DDT domain is named after (DNA binding homeobox and Different  Transcription factors) and is approximately 60 residues in length  [1]. Along with the WHIM motifs, it comprises an entirely alpha  helical module found in diverse eukaryotic chromatin proteins [2].  Based on the structure of Ioc3, this module is inferred to  interact with nucleosomal linker DNA and the SLIDE domain of ISWI  proteins [2][3]. The resulting complex forms a protein ruler that  measures out the spacing between two adjacent nucleosomes [2].  In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket [2].", "database": "PfamA", "aliStart": 241, "scoreName": "E-value", "accession": "PF02791.15", "start": 241, "score": 3.8e-17, "identifier": "DDT domain", "type": "DBD", "aliEnd": 297}}, {"startStyle": "straight", "end": 524, "endStyle": "straight", "aliStart": 456, "text": "WSD", "colour": "#9999ff", "aliEnd": 523, "start": 456, "href": "http://pfam.xfam.org/family/PF15613.4", "type": "pfama", "display": "true", "metadata": {"end": 524, "description": "This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins [1]. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [1,2]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes [2]. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA [1], and was first identified as WSD [3], the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.", "database": "PfamA", "aliStart": 456, "scoreName": "E-value", "accession": "PF15613.4", "start": 456, "score": 1.7e-08, "identifier": "Williams-Beuren syndrome DDT (WSD), D-TOX E motif", "type": "DBD", "aliEnd": 523}}, {"startStyle": "jagged", "end": 382, "endStyle": "straight", "aliStart": 356, "text": "WHIM1", "colour": "#9999ff", "aliEnd": 381, "start": 344, "href": "http://pfam.xfam.org/family/PF15612.4", "type": "pfama", "display": "true", "metadata": {"end": 382, "description": "A conserved alpha helical motif that along with the WHIM2 and  WHIM3 motifs, and the DDT domain comprise an alpha helical module  found in diverse eukaryotic chromatin proteins [1].Based on the  Ioc3 structure, this module is inferred to interact with nucleosomal  linker DNA and the SLIDE domain of ISWI proteins [1][2].  The resulting complex forms a protein ruler that measures out the  spacing between two adjacent nucleosomes [2]. The conserved basic  residue in WHIM1 is involved in packing with the DDT motif. The  module shows a great domain architectural diversity and is often  combined with other modified histone peptide recognising and  DNA binding domains, some of which discriminate methylated DNA [1].", "database": "PfamA", "aliStart": 356, "scoreName": "E-value", "accession": "PF15612.4", "start": 344, "score": 0.00016999999999999999, "identifier": "WSTF, HB1, Itc1p, MBD9 motif 1", "type": "DBD", "aliEnd": 381}}], "length": 2921}

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{"regions": [{"startStyle": "straight", "end": 2737, "endStyle": "straight", "aliStart": 2654, "text": "Bromodomain", "colour": "#9999ff", "aliEnd": 2736, "start": 2654, "href": "http://pfam.xfam.org/family/PF00439.23", "type": "pfama", "display": "true", "metadata": {"end": 2737, "description": "Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. 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The resulting complex forms a protein ruler that  measures out the spacing between two adjacent nucleosomes [2].  In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket [2].", "database": "PfamA", "aliStart": 102, "scoreName": "E-value", "accession": "PF02791.15", "start": 102, "score": 3.4999999999999996e-17, "identifier": "DDT domain", "type": "DBD", "aliEnd": 158}}, {"startStyle": "straight", "end": 385, "endStyle": "straight", "aliStart": 317, "text": "WSD", "colour": "#9999ff", "aliEnd": 384, "start": 317, "href": "http://pfam.xfam.org/family/PF15613.4", "type": "pfama", "display": "true", "metadata": {"end": 385, "description": "This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins [1]. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [1,2]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes [2]. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA [1], and was first identified as WSD [3], the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.", "database": "PfamA", "aliStart": 317, "scoreName": "E-value", "accession": "PF15613.4", "start": 317, "score": 1.6e-08, "identifier": "Williams-Beuren syndrome DDT (WSD), D-TOX E motif", "type": "DBD", "aliEnd": 384}}, {"startStyle": "jagged", "end": 243, "endStyle": "straight", "aliStart": 217, "text": "WHIM1", "colour": "#9999ff", "aliEnd": 242, "start": 205, "href": "http://pfam.xfam.org/family/PF15612.4", "type": "pfama", "display": "true", "metadata": {"end": 243, "description": "A conserved alpha helical motif that along with the WHIM2 and  WHIM3 motifs, and the DDT domain comprise an alpha helical module  found in diverse eukaryotic chromatin proteins [1].Based on the  Ioc3 structure, this module is inferred to interact with nucleosomal  linker DNA and the SLIDE domain of ISWI proteins [1][2].  The resulting complex forms a protein ruler that measures out the  spacing between two adjacent nucleosomes [2]. The conserved basic  residue in WHIM1 is involved in packing with the DDT motif. The  module shows a great domain architectural diversity and is often  combined with other modified histone peptide recognising and  DNA binding domains, some of which discriminate methylated DNA [1].", "database": "PfamA", "aliStart": 217, "scoreName": "E-value", "accession": "PF15612.4", "start": 205, "score": 0.00016, "identifier": "WSTF, HB1, Itc1p, MBD9 motif 1", "type": "DBD", "aliEnd": 242}}], "length": 2765}

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TF Info Page for BPTF (Unknown)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution