TF Info Page for VSX2 (Homeodomain)

Conclusion

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

Description

Description: visual system homeobox 2 [Source:HGNC Symbol;Acc:HGNC:1975]
Entrez Summary This gene encodes a homeobox protein originally described as a retina-specific transcription factor. Mutations in this gene are associated with microphthalmia, cataracts and iris abnormalities. [provided by RefSeq, Oct 2009]
Ensembl ID: ENSG00000119614
External Link: CisBP
Interpro IPR001356; IPR003654; IPR009057; IPR017970; IPR023339; ;
Protein Domain: ENSP00000261980
Domain:
Protein: ENSP00000261980DBD: HomeodomainOther: OAR

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:10903837 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" 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
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMZoo_01Inferred - vsx2 (98% AA Identity, Danio rerio)
PBMBarrera2016Inferred - VSX1 (91% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - VSX1 (91% AA Identity, Homo sapiens)
PBMBerger08Inferred - Vsx1 (91% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX1 (89% AA Identity, Homo sapiens)
B1HJASPARInferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Vsx2 (87% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Vsx1 (82% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx1 (82% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Vsx1 (82% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - ALX4 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx4 (78% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX4 (78% AA Identity, Homo sapiens)
B1HJASPARInferred - al (77% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - al (77% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - ALX1 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX1 (77% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx1 (77% AA Identity, Mus musculus)
PBMBerger08Inferred - Alx1 (77% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - ALX1 (77% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ALX1 (77% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (73% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (73% AA Identity, Mus musculus)
B1HJASPARInferred - Rx (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (73% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - UNCX (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - UNCX (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Uncx (73% AA Identity, Mus musculus)
PBMZoo_01Inferred - uncx4.1 (73% AA Identity, Tetraodon nigroviridis)
TransfacTransfacLicense requiredInferred - Arx (73% AA Identity, Rattus norvegicus)
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)
PBMBarrera2016Inferred - ARX (71% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (71% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (71% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (71% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (71% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - CG2808 (71% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Rax (71% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Rax (71% AA Identity, Rattus norvegicus)
B1HJASPARInferred - CG32532 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
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)
HT-SELEXYin2017Inferred - DMBX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DMBX1 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Dmbx1 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - DRGX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (68% AA Identity, Homo sapiens)
B1HJASPARInferred - PHDP (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - PHDP (68% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - PHOX2A (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2A (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2a (68% AA Identity, Mus musculus)
PBMBarrera2016Inferred - PHOX2B (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2b (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Drgx (68% AA Identity, Rattus norvegicus)
MiscHOMERInferred - Phox2a (68% AA Identity, Mus musculus)
SMiLE-seqIsakova2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX1 (67% AA Identity, Homo sapiens)
SMiLE-seqIsakova2017Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Gsc (66% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - PHOX2B (66% AA Identity, Homo sapiens)
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)
TransfacTransfacLicense requiredInferred - PROP1 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PROP1 (66% AA Identity, Sus scrofa)
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