Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Known motif
1 Monomer or homomultimer
High-throughput in vitro
Description
Description:
zinc finger homeobox 3 [Source:HGNC Symbol;Acc:HGNC:777]
Entrez Summary
#!usr/local/bin/perl
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This gene encodes a transcription factor with multiple homeodomains
and zinc finger motifs, and regulates myogenic and neuronal differentiation.
The encoded protein suppresses expression of the alpha-fetoprotein gene by
binding to an AT-rich enhancer motif. The protein has also been shown to
negatively regulate c-Myb, and transactivate the cell cycle inhibitor
cyclin-dependent kinase inhibitor 1A (also known as p21CIP1). This gene is
reported to function as a tumor suppressor in several cancers, and sequence
variants of this gene are also associated with atrial fibrillation. Multiple
transcript variants expressed from alternate promoters and encoding different
isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
Ensembl ID:
ENSG00000140836
External Link:
CisBP
Interpro
IPR001356 ; IPR003604 ; IPR007087 ; IPR009057 ; IPR015880 ; IPR017970 ;
Protein Domain:
ENSP00000268489
Protein Domain:
ENSP00000438926
Domain:
Protein: ENSP00000268489DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4, zf-Di19, zf-H2C2_5, zf-metProtein: ENSP00000438926DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4, zf-Di19, zf-met
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.
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:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:1719379 GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity TAS - PMID:1719379
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 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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Some member proteins, particularly those from plants, are annotated as being RNA-binding.", "database": "PfamA", "aliStart": 3468, "scoreName": "E-value", "accession": "PF12874.5", "start": 3465, "score": 2.0999999999999998e-09, "identifier": "Zinc-finger of C2H2 type", "type": "DBD", "aliEnd": 3486}}, {"startStyle": "straight", "end": 3553, "endStyle": "straight", "aliStart": 3529, "text": "zf-met", "colour": "#9999ff", "aliEnd": 3553, "start": 3529, "href": "http://pfam.xfam.org/family/PF12874.5", "type": "pfama", "display": "true", "metadata": {"end": 3553, "description": "This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.", "database": "PfamA", "aliStart": 3529, "scoreName": "E-value", "accession": "PF12874.5", "start": 3529, "score": 2.0999999999999998e-09, "identifier": "Zinc-finger of C2H2 type", "type": "DBD", "aliEnd": 3553}}, {"startStyle": "straight", "end": 1276, "endStyle": "straight", "aliStart": 1222, "text": "zf-Di19", "colour": "#9999ff", "aliEnd": 1273, "start": 1221, "href": "http://pfam.xfam.org/family/PF05605.10", "type": "pfama", "display": "true", "metadata": {"end": 1276, "description": "This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [1]. This domain is a zinc-binding domain.", "database": "PfamA", "aliStart": 1222, "scoreName": "E-value", "accession": "PF05605.10", "start": 1221, "score": 1.4000000000000001e-05, "identifier": "Drought induced 19 protein (Di19), zinc-binding", "type": "DBD", "aliEnd": 1273}}, {"startStyle": "straight", "end": 1247, "endStyle": "straight", "aliStart": 1223, "text": "zf-H2C2_5", "colour": "#9999ff", "aliEnd": 1247, "start": 1223, "href": "http://pfam.xfam.org/family/PF13909.4", "type": "pfama", "display": "true", "metadata": {"end": 1247, "description": NaN, "database": "PfamA", "aliStart": 1223, "scoreName": "E-value", "accession": "PF13909.4", "start": 1223, "score": 0.00047999999999999996, "identifier": "C2H2-type zinc-finger domain", "type": "DBD", "aliEnd": 1247}}], "length": 3704}
{"regions": [{"startStyle": "curved", "end": 1288, "endStyle": "curved", "aliStart": 1232, "text": "HD", "colour": "#228B22", "aliEnd": 1288, "start": 1232, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 1288, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. 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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. 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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": 1616, "scoreName": "E-value", "accession": "PF00096.24", "start": 1616, "score": 4.4e-11, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 1638}}, {"startStyle": "curved", "end": 1820, "endStyle": "curved", "aliStart": 1798, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 1820, "start": 1798, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 1820, "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": 1798, "scoreName": "E-value", "accession": "PF00096.24", "start": 1798, "score": 4.4e-11, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 1820}}, {"startStyle": "straight", "end": 332, "endStyle": "straight", "aliStart": 309, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 332, "start": 309, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 332, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 309, "scoreName": "E-value", "accession": "PF13894.4", "start": 309, "score": 5.6e-13, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 332}}, {"startStyle": "straight", "end": 1092, "endStyle": "straight", "aliStart": 1070, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 1092, "start": 1069, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 1092, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 1070, "scoreName": "E-value", "accession": "PF13894.4", "start": 1069, "score": 5.6e-13, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 1092}}, {"startStyle": "jagged", "end": 2572, "endStyle": "straight", "aliStart": 2554, "text": "zf-met", "colour": "#9999ff", "aliEnd": 2572, "start": 2551, "href": "http://pfam.xfam.org/family/PF12874.5", "type": "pfama", "display": "true", "metadata": {"end": 2572, "description": "This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.", "database": "PfamA", "aliStart": 2554, "scoreName": "E-value", "accession": "PF12874.5", "start": 2551, "score": 6.1e-06, "identifier": "Zinc-finger of C2H2 type", "type": "DBD", "aliEnd": 2572}}, {"startStyle": "straight", "end": 2639, "endStyle": "straight", "aliStart": 2615, "text": "zf-met", "colour": "#9999ff", "aliEnd": 2639, "start": 2615, "href": "http://pfam.xfam.org/family/PF12874.5", "type": "pfama", "display": "true", "metadata": {"end": 2639, "description": "This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.", "database": "PfamA", "aliStart": 2615, "scoreName": "E-value", "accession": "PF12874.5", "start": 2615, "score": 6.1e-06, "identifier": "Zinc-finger of C2H2 type", "type": "DBD", "aliEnd": 2639}}, {"startStyle": "straight", "end": 362, "endStyle": "straight", "aliStart": 308, "text": "zf-Di19", "colour": "#9999ff", "aliEnd": 359, "start": 307, "href": "http://pfam.xfam.org/family/PF05605.10", "type": "pfama", "display": "true", "metadata": {"end": 362, "description": "This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [1]. This domain is a zinc-binding domain.", "database": "PfamA", "aliStart": 308, "scoreName": "E-value", "accession": "PF05605.10", "start": 307, "score": 1.1e-05, "identifier": "Drought induced 19 protein (Di19), zinc-binding", "type": "DBD", "aliEnd": 359}}], "length": 2790}