The Human Transcription Factors

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	TBA
Ensembl ID:	ENSG00000123636
External Link:	T113537_1.02
Interpro	IPR001487; IPR001739; IPR001965; IPR004022; IPR011011; IPR016177; IPR018359; IPR018500; IPR018501; IPR019787;
Protein Domain:
Protein: ENSP00000376533	DBD: Methyl-CpG DNA-binding	Other: Bromodomain, DDT, Nop14, PHD, WSD
Protein: ENSP00000400505	DBD: Methyl-CpG DNA-binding	Other:
Protein: ENSP00000393565	DBD: Methyl-CpG DNA-binding	Other:

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

Source	Annotation	Motif	Evidence

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

{"regions": [{"startStyle": "curved", "end": 789, "endStyle": "jagged", "aliStart": 739, "text": "MBD", "colour": "#2cb42c", "aliEnd": 786, "start": 737, "href": "http://pfam.xfam.org/family/PF01429.17", "type": "pfama", "display": "true", "metadata": {"end": 789, "description": "The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1].  DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair [1]. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase [2].", "database": "PfamA", "aliStart": 739, "scoreName": "E-value", "accession": "PF01429.17", "start": 737, "score": 2.3e-14, "identifier": "Methyl-CpG binding domain", "type": "DBD", "aliEnd": 786}}, {"startStyle": "straight", "end": 2115, "endStyle": "straight", "aliStart": 2033, "text": "Bromodomain", "colour": "#9999ff", "aliEnd": 2111, "start": 2033, "href": "http://pfam.xfam.org/family/PF00439.23", "type": "pfama", "display": "true", "metadata": {"end": 2115, "description": "Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].", "database": "PfamA", "aliStart": 2033, "scoreName": "E-value", "accession": "PF00439.23", "start": 2033, "score": 5.0000000000000005e-21, "identifier": "Bromodomain", "type": "DBD", "aliEnd": 2111}}, {"startStyle": "straight", "end": 1439, "endStyle": "jagged", "aliStart": 1337, "text": "WSD", "colour": "#9999ff", "aliEnd": 1394, "start": 1336, "href": "http://pfam.xfam.org/family/PF15613.4", "type": "pfama", "display": "true", "metadata": {"end": 1439, "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": 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}

TF Info Page for BAZ2B (MBD)