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
Description
Description:
IKAROS family zinc finger 1 [Source:HGNC Symbol;Acc:HGNC:13176]
Entrez Summary
#!usr/local/bin/perl
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This gene encodes a transcription factor that belongs to the family
of zinc-finger DNA-binding proteins associated with chromatin remodeling. The
expression of this protein is restricted to the fetal and adult
hemo-lymphopoietic system, and it functions as a regulator of lymphocyte
differentiation. Several alternatively spliced transcript variants encoding
different isoforms have been described for this gene. Most isoforms share a
common C-terminal domain, which contains two zinc finger motifs that are
required for hetero- or homo-dimerization, and for interactions with other
proteins. The isoforms, however, differ in the number of N-terminal zinc
finger motifs that bind DNA and in nuclear localization signal presence,
resulting in members with and without DNA-binding properties. Only a few
isoforms contain the requisite three or more N-terminal zinc motifs that
confer high affinity binding to a specific core DNA sequence element in the
promoters of target genes. The non-DNA-binding isoforms are largely found in
the cytoplasm, and are thought to function as dominant-negative factors.
Overexpression of some dominant-negative isoforms have been associated with
B-cell malignancies, such as acute lymphoblastic leukemia (ALL). [provided by
RefSeq, May 2014]
Ensembl ID:
ENSG00000185811
External Link:
CisBP
Interpro
IPR007087 ; IPR015880 ;
Protein Domain:
ENSP00000331614
Protein Domain:
ENSP00000352123
Protein Domain:
ENSP00000388478
Protein Domain:
ENSP00000409588
Protein Domain:
ENSP00000413025
Protein Domain:
ENSP00000483016
Protein Domain:
ENSP00000396554
Domain:
Protein: ENSP00000331614DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4Protein: ENSP00000352123DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4Protein: ENSP00000388478DBD: C2H2 ZF Containing ProteinsOther: Protein: ENSP00000409588DBD: C2H2 ZF Containing ProteinsOther: Protein: ENSP00000413025DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4Protein: ENSP00000483016DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4Protein: ENSP00000396554DBD: C2H2 ZF Containing ProteinsOther: zf-C2H2_4
Previous Annotations
Source
Annotation
TF-CAT classification
TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:15841184
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 IBA - GO_REF:0000033
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
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. 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": 448, "scoreName": "E-value", "accession": "PF00096.24", "start": 448, "score": 2.4e-12, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 472}}, {"startStyle": "straight", "end": 440, "endStyle": "jagged", "aliStart": 420, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 439, "start": 420, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 440, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 420, "scoreName": "E-value", "accession": "PF13894.4", "start": 420, "score": 7.6e-09, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 439}}], "length": 478}
{"regions": [{"startStyle": "curved", "end": 100, "endStyle": "curved", "aliStart": 78, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 100, "start": 78, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 100, "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": 78, "scoreName": "E-value", "accession": "PF00096.24", "start": 78, "score": 1.1e-07, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 100}}, {"startStyle": "curved", "end": 263, "endStyle": "curved", "aliStart": 239, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 263, "start": 239, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 263, "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": 239, "scoreName": "E-value", "accession": "PF00096.24", "start": 239, "score": 1.1e-07, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 263}}, {"startStyle": "straight", "end": 231, "endStyle": "jagged", "aliStart": 211, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 230, "start": 211, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 231, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 211, "scoreName": "E-value", "accession": "PF13894.4", "start": 211, "score": 5.1e-07, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 230}}], "length": 269}
{"regions": [{"startStyle": "curved", "end": 80, "endStyle": "curved", "aliStart": 58, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 80, "start": 58, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 80, "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": 58, "scoreName": "E-value", "accession": "PF00096.24", "start": 58, "score": 1e-14, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 80}}, {"startStyle": "curved", "end": 108, "endStyle": "curved", "aliStart": 86, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 108, "start": 86, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 108, "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": 86, "scoreName": "E-value", "accession": "PF00096.24", "start": 86, "score": 1e-14, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 108}}, {"startStyle": "curved", "end": 137, "endStyle": "curved", "aliStart": 114, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 137, "start": 114, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 137, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. 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