TF Info Page for SIX3 (Homeodomain)

Conclusion

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

Description

Description: SIX homeobox 3 [Source:HGNC Symbol;Acc:HGNC:10889]
Entrez Summary This gene encodes a member of the sine oculis homeobox transcription factor family. The encoded protein plays a role in eye development. Mutations in this gene have been associated with holoprosencephaly type 2. [provided by RefSeq, Oct 2009]
Ensembl ID: ENSG00000138083
External Link: CisBP
Interpro IPR001356; IPR009057;
Protein Domain: ENSP00000260653
Domain:
Protein: ENSP00000260653DBD: HomeodomainOther: SIX1_SD

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_Co-activation_
PMIDS:12543801
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:0001205
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involv
IEA - GO_REF:0000019
GO:0003700
sequence-specific DNA binding transcription factor activity
ISS - GO_REF:0000024
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-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
PBMBerger08Inferred - Six3 (100% AA Identity, Mus musculus)
PBMBarrera2016Inferred - SIX6 (98% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - SIX6 (98% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SIX6 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SIX6 (98% AA Identity, Homo sapiens)
PBMBadis09Inferred - Six6 (98% AA Identity, Mus musculus)
PBMBerger08Inferred - Six6 (98% AA Identity, Mus musculus)
PBMBarrera2016Inferred - SIX6 (96% AA Identity, Homo sapiens)
B1HJASPARInferred - Optix (94% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Optix (94% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Optix (94% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - six3 (94% AA Identity, Oryzias latipes)
HT-SELEXYin2017Inferred - SIX2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SIX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SIX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SIX2 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Six2 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - SIX1 (67% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - SIX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SIX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SIX1 (67% AA Identity, Homo sapiens)
PBMBerger08Inferred - Six1 (67% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - SIX1 (67% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - SIX1 (67% AA Identity, Homo sapiens)
MiscHOMERInferred - Six1 (67% AA Identity, Mus musculus)
B1HJASPARInferred - so (65% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - so (65% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - so (65% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - so (65% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - so (65% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - so (65% AA Identity, Drosophila melanogaster)

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