TF Info Page for RAX2 (Homeodomain)

Conclusion

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

Description

Description: retina and anterior neural fold homeobox 2 [Source:HGNC Symbol;Acc:HGNC:18286]
Entrez Summary This gene encodes a homeodomain-containing protein that plays a role in eye development. Mutation of this gene causes age-related macular degeneration type 6, an eye disorder resulting in accumulations of protein and lipid beneath the retinal pigment epithelium and within the Bruch's membrane. Defects in this gene can also cause cone-rod dystrophy type 11, a disease characterized by the initial degeneration of cone photoreceptor cells and resulting in loss of color vision and visual acuity, followed by the degeneration of rod photoreceptor cells, which progresses to night blindness and the loss of peripheral vision. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Ensembl ID: ENSG00000173976
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; ;
Protein Domain: ENSP00000450456
Protein Domain: ENSP00000450687
Domain:
Protein: ENSP00000450456DBD: HomeodomainOther:
Protein: ENSP00000450687DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification No
PMIDS:
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.
b
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
HT-SELEXJolma2013Direct
HT-SELEXYin2017Inferred - RAX (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - RAX (92% AA Identity, Homo sapiens)
PBMBerger08Inferred - Rax (92% AA Identity, Mus musculus)
B1HJASPARInferred - Rx (92% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (92% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (92% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Rax (92% AA Identity, Rattus norvegicus)
B1HJASPARInferred - hbn (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - hbn (73% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - ARX (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (71% AA Identity, Mus musculus)
B1HJASPARInferred - CG9876 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (71% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Arx (71% AA Identity, Rattus norvegicus)
HT-SELEXYin2017Inferred - ALX4 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx4 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - ARX (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (70% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - CG2808 (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - DRGX (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (70% AA Identity, Homo sapiens)
B1HJASPARInferred - Pph13 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Pph13 (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Prrx2 (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)
PBMBerger08Inferred - Vsx1 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX2 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ALX4 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Drgx (70% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - PRRX2 (70% AA Identity, Homo sapiens)
SELEXJASPARInferred - Prrx2 (70% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Prrx2 (70% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - PRRX2 (70% AA Identity, Sus scrofa)
TransfacTransfacLicense requiredInferred - VSX2 (70% AA Identity, Homo sapiens)
MiscHocoMocoInferred - PRRX2 (70% AA Identity, Homo sapiens)
MiscHocoMocoInferred - VSX2 (70% AA Identity, Homo sapiens)
B1HJASPARInferred - al (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - al (68% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - ALX3 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX3 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx3 (68% AA Identity, Mus musculus)
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)
PBMBerger08Inferred - Prrx1 (68% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX1 (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - VSX1 (68% AA Identity, Homo sapiens)
PBMZoo_01Inferred - vsx2 (68% AA Identity, Danio rerio)
TransfacTransfacLicense requiredInferred - PRRX1 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Prrx1 (68% AA Identity, Rattus norvegicus)
MiscHOMERInferred - Phox2a (68% AA Identity, Mus musculus)
MiscHocoMocoInferred - PRRX1 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX1 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx1 (66% AA Identity, Mus musculus)
PBMBerger08Inferred - Alx1 (66% AA Identity, Mus musculus)
B1HJASPARInferred - CG11294 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (66% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG32532 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32532 (66% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - ISX (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ISX (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ISX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (66% AA Identity, Homo sapiens)
B1HJASPARInferred - PHDP (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - PHDP (66% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - PHOX2B (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - UNCX (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - UNCX (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Uncx (66% AA Identity, Mus musculus)
PBMZoo_01Inferred - uncx4.1 (66% AA Identity, Tetraodon nigroviridis)
PBMBarrera2016Inferred - VSX1 (66% AA Identity, Homo sapiens)
B1HJASPARInferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Vsx2 (66% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ALX1 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ALX1 (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