Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Known motif
1 Monomer or homomultimer
High-throughput in vitro
Has a putative AT-hook
Description
Description:
CCCTC-binding factor [Source:HGNC Symbol;Acc:HGNC:13723]
Entrez Summary
#!usr/local/bin/perl
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This gene is a member of the BORIS + CTCF gene family and encodes a
transcriptional regulator protein with 11 highly conserved zinc finger (ZF)
domains. This nuclear protein is able to use different combinations of the ZF
domains to bind different DNA target sequences and proteins. Depending upon
the context of the site, the protein can bind a histone acetyltransferase
(HAT)-containing complex and function as a transcriptional activator or bind
a histone deacetylase (HDAC)-containing complex and function as a
transcriptional repressor. If the protein is bound to a transcriptional
insulator element, it can block communication between enhancers and upstream
promoters, thereby regulating imprinted expression. Mutations in this gene
have been associated with invasive breast cancers, prostate cancers, and
Wilms' tumors. Alternatively spliced transcript variants encoding different
isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
Ensembl ID:
ENSG00000102974
External Link:
CisBP
Interpro
IPR007087 ; IPR015880 ;
Protein Domain:
ENSP00000264010
Protein Domain:
ENSP00000384707
Domain:
Protein: ENSP00000264010DBD: C2H2 ZF Containing ProteinsOther: Protein: ENSP00000384707DBD: C2H2 ZF Containing ProteinsOther:
Previous Annotations
Source
Annotation
TF-CAT classification
TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:8246978 15143173
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.
a
CisBP considers it as a TF?
Yes
TFclass considers it as a TF?
Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"
Yes
GO-Info
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IDA - PMID:8649389 GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IEA - GO_REF:0000019 GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:8649389, PMID:9591631
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
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements
DNA-Binding
Published Motif Data
Structure
Experimental History
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The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 468, "scoreName": "E-value", "accession": "PF00096.24", "start": 467, "score": 8.5e-34, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 489}}, {"startStyle": "curved", "end": 517, "endStyle": "curved", "aliStart": 495, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 517, "start": 495, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 517, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. 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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. 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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 555, "scoreName": "E-value", "accession": "PF00096.24", "start": 555, "score": 8.5e-34, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 573}}], "length": 728}
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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 140, "scoreName": "E-value", "accession": "PF00096.24", "start": 139, "score": 5.7e-24, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 161}}, {"startStyle": "curved", "end": 189, "endStyle": "curved", "aliStart": 167, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 189, "start": 167, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 189, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 167, "scoreName": "E-value", "accession": "PF00096.24", "start": 167, "score": 5.7e-24, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 189}}, {"startStyle": "curved", "end": 218, "endStyle": "curved", "aliStart": 195, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 218, "start": 195, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 218, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 195, "scoreName": "E-value", "accession": "PF00096.24", "start": 195, "score": 5.7e-24, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 218}}, {"startStyle": "curved", "end": 247, "endStyle": "jagged", "aliStart": 227, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 245, "start": 227, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 247, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 227, "scoreName": "E-value", "accession": "PF00096.24", "start": 227, "score": 5.7e-24, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 245}}], "length": 400}