The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro	ChIP-seq motif is consistent with recognition code (RCADE)

Description

Description:

IKAROS family zinc finger 3 [Source:HGNC Symbol;Acc:HGNC:13178]

Entrez Summary

This gene encodes a member of the Ikaros family of zinc-finger proteins. Three members of this protein family (Ikaros, Aiolos and Helios) are hematopoietic-specific transcription factors involved in the regulation of lymphocyte development. This gene product is a transcription factor that is important in the regulation of B lymphocyte proliferation and differentiation. Both Ikaros and Aiolos can participate in chromatin remodeling. Regulation of gene expression in B lymphocytes by Aiolos is complex as it appears to require the sequential formation of Ikaros homodimers, Ikaros/Aiolos heterodimers, and Aiolos homodimers. Several alternative transcripts encoding different isoforms have been described, as well as some non-protein coding variants. [provided by RefSeq, Apr 2012]

Ensembl ID:

ENSG00000161405

External Link:

CisBP

Interpro

IPR007087; IPR015880;

Protein Domain:

ENSP00000344544

Protein Domain:

ENSP00000367179

Protein Domain:

ENSP00000367180

Protein Domain:

ENSP00000367188

Protein Domain:

ENSP00000367194

Protein Domain:

ENSP00000377741

Protein Domain:

ENSP00000403776

Protein Domain:

ENSP00000438972

Protein Domain:

ENSP00000485515

Protein Domain:

ENSP00000462452

Domain:

Protein: ENSP00000344544	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4
Protein: ENSP00000367179	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4
Protein: ENSP00000367180	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000367188	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000367194	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4
Protein: ENSP00000377741	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000403776	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4
Protein: ENSP00000438972	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4
Protein: ENSP00000485515	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000462452	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_Transcription Factor Binding tf co-factor binding DNA-Binding sequence-specific_DNA Binding TF PPI Transactivation_ PMIDS:9155026
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: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 TAS - PMID:10552935
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

Source	Annotation	Motif	Evidence
RCADE	Schmitges2016		Direct
Transfac	Transfac	License required	Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - IKZF1 (81% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF2 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IKZF2 (78% AA Identity, Homo sapiens)

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

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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": 146, "scoreName": "E-value", "accession": "PF00096.24", "start": 146, "score": 1.9e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 168}}, {"startStyle": "curved", "end": 196, "endStyle": "curved", "aliStart": 174, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 196, "start": 174, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 196, "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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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": 140, "score": 2.0000000000000002e-11, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 162}}, {"startStyle": "curved", "end": 431, "endStyle": "curved", "aliStart": 407, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 431, "start": 407, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 431, "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": 407, "scoreName": "E-value", "accession": "PF00096.24", "start": 407, "score": 2.0000000000000002e-11, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 431}}, {"startStyle": "straight", "end": 399, "endStyle": "jagged", "aliStart": 379, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 398, "start": 379, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 399, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 379, "scoreName": "E-value", "accession": "PF13894.4", "start": 379, "score": 2.8000000000000003e-09, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 398}}], "length": 437}

{"regions": [{"startStyle": "jagged", "end": 106, "endStyle": "curved", "aliStart": 86, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 106, "start": 84, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 106, "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": 84, "score": 1.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 106}}, {"startStyle": "curved", "end": 134, "endStyle": "curved", "aliStart": 112, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 134, "start": 112, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 134, "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": 112, "scoreName": "E-value", "accession": "PF00096.24", "start": 112, "score": 1.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 134}}, {"startStyle": "curved", "end": 162, "endStyle": "curved", "aliStart": 140, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 162, "start": 140, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 162, "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": 140, "scoreName": "E-value", "accession": "PF00096.24", "start": 140, "score": 1.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 162}}, {"startStyle": "curved", "end": 189, "endStyle": "curved", "aliStart": 168, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 187, "start": 168, "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": 168, "scoreName": "E-value", "accession": "PF00096.24", "start": 168, "score": 1.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 187}}, {"startStyle": "curved", "end": 470, "endStyle": "curved", "aliStart": 446, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 470, "start": 446, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 470, "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": 446, "scoreName": "E-value", "accession": "PF00096.24", "start": 446, "score": 1.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 470}}, {"startStyle": "straight", "end": 438, "endStyle": "jagged", "aliStart": 418, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 437, "start": 418, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 438, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 418, "scoreName": "E-value", "accession": "PF13894.4", "start": 418, "score": 3.4e-11, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 437}}], "length": 476}

TF Info Page for IKZF3 (C2H2 ZF(non-KRAB))

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution