Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Likely to be sequence specific TF
3 Low specificity DNA-binding protein
No motif
Has a putative AT-hook
Description
Description:
bromodomain adjacent to zinc finger domain 2B [Source:HGNC Symbol;Acc:HGNC:963]
Entrez Summary
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This gene belongs to the bromodomain gene family. Members of this
gene family encode proteins that are integral components of chromatin
remodeling complexes. The encoded protein showed strong preference for the
activating H3K14Ac mark in a histone peptide screen, suggesting a potential
role in transcriptional activation. This gene may be associated with
susceptibility to sudden cardiac death (SCD). [provided by RefSeq, Aug 2016]
Ensembl ID:
ENSG00000123636
External Link:
CisBP
Interpro
IPR001487 ; IPR001739 ; IPR001965 ; IPR004022 ; IPR011011 ; IPR016177 ; IPR018359 ; IPR018500 ; IPR018501 ; IPR019787 ;
Protein Domain:
ENSP00000376533
Protein Domain:
ENSP00000400505
Protein Domain:
ENSP00000393565
Domain:
Protein: ENSP00000376533DBD: Methyl-CpG DNA-bindingOther: Bromodomain, DDT, Nop14, PHD, WSDProtein: ENSP00000400505DBD: Methyl-CpG DNA-bindingOther: Protein: ENSP00000393565DBD: Methyl-CpG DNA-bindingOther:
Previous Annotations
Source
Annotation
TF-CAT classification
No PMIDS:
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.
x
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
4a, two or more datasets predict it as a TF
TF has conditional DNA-binding requirements
DNA-Binding
Published Motif Data
Structure
Experimental History
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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": 1337, "scoreName": "E-value", "accession": "PF15613.4", "start": 1336, "score": 1.1999999999999999e-11, "identifier": "Williams-Beuren syndrome DDT (WSD), D-TOX E motif", "type": "DBD", "aliEnd": 1394}}, {"startStyle": "jagged", "end": 1716, "endStyle": "straight", "aliStart": 1679, "text": "WSD", "colour": "#9999ff", "aliEnd": 1715, "start": 1647, "href": "http://pfam.xfam.org/family/PF15613.4", "type": "pfama", "display": "true", "metadata": {"end": 1716, "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": 1679, "scoreName": "E-value", "accession": "PF15613.4", "start": 1647, "score": 1.1999999999999999e-11, "identifier": "Williams-Beuren syndrome DDT (WSD), D-TOX E motif", "type": "DBD", "aliEnd": 1715}}, {"startStyle": "straight", "end": 1945, "endStyle": "straight", "aliStart": 1897, "text": "PHD", "colour": "#9999ff", "aliEnd": 1944, "start": 1897, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1945, "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": 1897, "scoreName": "E-value", "accession": "PF00628.27", "start": 1897, "score": 1.2999999999999999e-11, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1944}}, {"startStyle": "straight", "end": 1113, "endStyle": "straight", "aliStart": 1053, "text": "DDT", "colour": "#9999ff", "aliEnd": 1113, "start": 1052, "href": "http://pfam.xfam.org/family/PF02791.15", "type": "pfama", "display": "true", "metadata": {"end": 1113, "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": 1053, "scoreName": "E-value", "accession": "PF02791.15", "start": 1052, "score": 3.1e-09, "identifier": "DDT domain", "type": "DBD", "aliEnd": 1113}}, {"startStyle": "jagged", "end": 382, "endStyle": "jagged", "aliStart": 224, "text": "Nop14", "colour": "#9999ff", "aliEnd": 363, "start": 191, "href": "http://pfam.xfam.org/family/PF04147.10", "type": "pfama", "display": "true", "metadata": {"end": 382, "description": "Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [1].", "database": "PfamA", "aliStart": 224, "scoreName": "E-value", "accession": "PF04147.10", "start": 191, "score": 5.7000000000000005e-06, "identifier": "Nop14-like family ", "type": "DBD", "aliEnd": 363}}, {"startStyle": "jagged", "end": 806, "endStyle": "jagged", "aliStart": 597, "text": "Nop14", "colour": "#9999ff", "aliEnd": 669, "start": 558, "href": "http://pfam.xfam.org/family/PF04147.10", "type": "pfama", "display": "true", "metadata": {"end": 806, "description": "Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [1].", "database": "PfamA", "aliStart": 597, "scoreName": "E-value", "accession": "PF04147.10", "start": 558, "score": 5.7000000000000005e-06, "identifier": "Nop14-like family ", "type": "DBD", "aliEnd": 669}}], "length": 2133}
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