TF Info Page for PAX6 (Homeodomain; Paired box)

Conclusion

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

Description

Description: paired box 6 [Source:HGNC Symbol;Acc:HGNC:8620]
Entrez Summary This gene encodes a homeobox and paired domain-containing protein that binds DNA and functions as a regulator of transcription. Activity of this protein is key in the development of neural tissues, particularly the eye. This gene is regulated by multiple enhancers located up to hundreds of kilobases distant from this locus. Mutations in this gene or in the enhancer regions can cause ocular disorders such as aniridia and Peter's anomaly. Use of alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2015]
Ensembl ID: ENSG00000007372
External Link: CisBP
Interpro IPR001356; IPR001523; IPR009057; IPR017970;
Protein Domain: ENSP00000241001
Protein Domain: ENSP00000368406
Protein Domain: ENSP00000368410
Protein Domain: ENSP00000368418
Protein Domain: ENSP00000404100
Protein Domain: ENSP00000480026
Protein Domain: ENSP00000368403
Protein Domain: ENSP00000404356
Protein Domain: ENSP00000388132
Protein Domain: ENSP00000436365
Domain:
Protein: ENSP00000241001DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000368406DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000368410DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000368418DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000404100DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000480026DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000368403DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000404356DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000388132DBD: Homeodomain,Paired boxOther:
Protein: ENSP00000436365DBD: Homeodomain,Paired boxOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_Transactivation_
PMIDS:7753864 7841787 8132558 9710641 12756174
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:0000981
sequence-specific DNA binding RNA polymerase II transcription factor activity
IDA - PMID:20592023
GO:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IEA - GO_REF:0000019
GO:0001227
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:10441571, PMID:10747901
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
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
SELEXJASPARDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMBerger08Inferred - Pax6 (100% AA Identity, Mus musculus)
HT-SELEXNitta2015Inferred - ey (93% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - ey (93% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - ey (93% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - toy (90% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - toy (90% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - toy (90% AA Identity, Drosophila melanogaster)

Structure

Structure PDB 6PAX

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