TF Info Page for ZIC4 (C2H2 ZF)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro

Description

Description: Zic family member 4 [Source:HGNC Symbol;Acc:HGNC:20393]
Entrez Summary This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. Members of this family are important during development, and have been associated with X-linked visceral heterotaxy and holoprosencephaly type 5. This gene is closely linked to the gene encoding zinc finger protein of the cerebellum 1, a related family member on chromosome 3. Heterozygous deletion of these linked genes is involved in Dandy-Walker malformation, which is a congenital cerebellar malformation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Dec 2009]
Ensembl ID: ENSG00000174963
External Link: CisBP
Interpro IPR007087; IPR015880;
Protein Domain: ENSP00000372553
Protein Domain: ENSP00000420627
Protein Domain: ENSP00000397695
Protein Domain: ENSP00000420775
Protein Domain: ENSP00000417855
Protein Domain: ENSP00000435509
Domain:
Protein: ENSP00000372553DBD: C2H2 ZF Containing ProteinsOther:
Protein: ENSP00000420627DBD: C2H2 ZF Containing ProteinsOther:
Protein: ENSP00000397695DBD: C2H2 ZF Containing ProteinsOther:
Protein: ENSP00000420775DBD: C2H2 ZF Containing ProteinsOther:
Protein: ENSP00000417855DBD: C2H2 ZF Containing ProteinsOther:
Protein: ENSP00000435509DBD: C2H2 ZF Containing ProteinsOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_DNA-Binding
sequence-specific_Other_
PMIDS:15338008 15465018
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.
b
CisBP considers it as a TF? Yes
TFclass considers it as a TF? Yes
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
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
HT-SELEXYin2017Inferred - ZIC1 (89% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ZIC1 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ZIC1 (89% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ZIC1 (89% AA Identity, Homo sapiens)
PBMBadis09Inferred - Zic1 (89% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ZIC1 (89% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ZIC1 (89% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ZIC1 (89% AA Identity, Homo sapiens)
PBMBadis09Inferred - Zic2 (88% AA Identity, Mus musculus)
ChIP-seqNajafabadi2015Inferred - ZIC2 (88% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ZIC2 (88% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ZIC2 (88% AA Identity, Homo sapiens)
PBMDREAM_contestInferred - Zic5 (87% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - ZIC5 (86% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ZIC5 (86% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ZIC3 (84% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ZIC3 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ZIC3 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ZIC3 (84% AA Identity, Homo sapiens)
PBMBadis09Inferred - Zic3 (84% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ZIC3 (84% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ZIC3 (84% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ZIC3 (84% AA Identity, Homo sapiens)
SELEXJASPARInferred - Macho-1 (72% AA Identity, Halocynthia roretzi)

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