TF Info Page for VSX1 (Homeodomain)

Conclusion

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

Description

Description: visual system homeobox 1 [Source:HGNC Symbol;Acc:HGNC:12723]
Entrez Summary The protein encoded by this gene contains a paired-like homeodomain and binds to the core of the locus control region of the red/green visual pigment gene cluster. The encoded protein may regulate expression of the cone opsin genes early in development. Mutations in this gene can cause posterior polymorphous corneal dystrophy and keratoconus. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000100987
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR023339;
Protein Domain: ENSP00000365897
Protein Domain: ENSP00000365899
Protein Domain: ENSP00000401690
Protein Domain: ENSP00000387720
Domain:
Protein: ENSP00000365897DBD: HomeodomainOther:
Protein: ENSP00000365899DBD: HomeodomainOther:
Protein: ENSP00000401690DBD: HomeodomainOther:
Protein: ENSP00000387720DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:11978762 15647262
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:0003700
sequence-specific DNA binding transcription factor activity
NAS - PMID:10673340
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
SMiLE-seqIsakova2017Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
B1HJASPARInferred - Vsx2 (82% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (82% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (82% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Vsx2 (82% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Vsx1 (77% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx1 (77% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Vsx1 (77% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - al (75% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - al (75% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - ALX1 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX1 (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx1 (75% AA Identity, Mus musculus)
PBMBerger08Inferred - Alx1 (75% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX1 (75% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ALX1 (75% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx4 (73% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX4 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Vsx1 (72% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx3 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - UNCX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - UNCX (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Uncx (71% AA Identity, Mus musculus)
PBMZoo_01Inferred - uncx4.1 (71% AA Identity, Tetraodon nigroviridis)
HT-SELEXNitta2015Inferred - CG2808 (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG32532 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - RAX (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Rax (70% AA Identity, Mus musculus)
B1HJASPARInferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - repo (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - repo (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Rx (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (70% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Rax (70% AA Identity, Rattus norvegicus)
PBMBarrera2016Inferred - ARX (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - DMBX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DMBX1 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Dmbx1 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Arx (68% AA Identity, Rattus norvegicus)
PBMBarrera2016Inferred - VSX2 (67% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (67% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (67% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - VSX2 (67% AA Identity, Homo sapiens)
MiscHocoMocoInferred - VSX2 (67% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - DRGX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (66% AA Identity, Homo sapiens)
B1HJASPARInferred - PHDP (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - PHDP (66% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - PHOX2A (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2A (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2a (66% AA Identity, Mus musculus)
PBMBarrera2016Inferred - PHOX2B (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2b (66% AA Identity, Mus musculus)
B1HJASPARInferred - Pph13 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Pph13 (66% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PROP1 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Prop1 (66% AA Identity, Mus musculus)
PBMZoo_01Inferred - vsx2 (66% AA Identity, Danio rerio)
TransfacTransfacLicense requiredInferred - Drgx (66% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - PROP1 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PROP1 (66% AA Identity, Sus scrofa)
MiscHOMERInferred - Phox2a (66% AA Identity, Mus musculus)
MiscHocoMocoInferred - PROP1 (66% 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