TF Info Page for VAX1 (Homeodomain)

Conclusion

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

Description

Description: ventral anterior homeobox 1 [Source:HGNC Symbol;Acc:HGNC:12660]
Entrez Summary This gene encodes a homeo-domain containing protein from a class of homeobox transcription factors which are conserved in vertebrates. Genes of this family are involved in the regulation of body development and morphogenesis. The most conserved genes, called HOX genes are found in special gene clusters. This gene belongs to the VAX subfamily and lies in the vicinity of the EMX homeobox gene family. Another member of VAX family is located on chromosome 2. The encoded protein may play an important role in the development of anterior ventral forebrain and visual system. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000148704
External Link: CisBP
Interpro IPR000047; IPR001356; IPR009057; IPR017970;
Protein Domain: ENSP00000277905
Protein Domain: ENSP00000358207
Domain:
Protein: ENSP00000277905DBD: HomeodomainOther:
Protein: ENSP00000358207DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_Transcription Factor Binding
tf co-factor binding_TF PPI_
PMIDS:15322073
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:0001227
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor
IEA - GO_REF:0000019
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
PBMBerger08Inferred - Vax1 (100% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VAX2 (100% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VAX2 (100% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VAX2 (100% AA Identity, Homo sapiens)
PBMBerger08Inferred - Vax2 (100% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Vax1 (100% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VAX2 (98% 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