TF Info Page for RAX (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 [Source:HGNC Symbol;Acc:HGNC:18662]
Entrez Summary This gene encodes a homeobox-containing transcription factor that functions in eye development. The gene is expressed early in the eye primordia, and is required for retinal cell fate determination and also regulates stem cell proliferation. Mutations in this gene have been reported in patients with defects in ocular development, including microphthalmia, anophthalmia, and coloboma.[provided by RefSeq, Oct 2009]
Ensembl ID: ENSG00000134438
External Link: CisBP
Interpro IPR001356; IPR003654; IPR009057; IPR017970;
Protein Domain: ENSP00000256852
Protein Domain: ENSP00000334813
Protein Domain: ENSP00000450583
Domain:
Protein: ENSP00000256852DBD: HomeodomainOther:
Protein: ENSP00000334813DBD: HomeodomainOther: OAR
Protein: ENSP00000450583DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_Transcription Factor Binding
tf co-factor binding_TF PPI_
PMIDS:11069920 10625658 10625658 10625658 10625658 11069920
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:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IDA - PMID:10625658
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-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBerger08Inferred - Rax (100% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Rax (100% AA Identity, Rattus norvegicus)
B1HJASPARInferred - Rx (98% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (98% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (98% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - ARX (75% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (75% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Arx (75% AA Identity, Rattus norvegicus)
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)
PBMBarrera2016Inferred - ARX (73% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (73% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (73% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (73% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (73% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - CG2808 (73% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - hbn (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - hbn (73% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - repo (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - repo (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - repo (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - repo (73% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ALX4 (73% AA Identity, Homo sapiens)
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 - DRGX (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (71% AA Identity, Homo sapiens)
B1HJASPARInferred - Pph13 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Pph13 (71% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PRRX2 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Prrx2 (71% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Drgx (71% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - PRRX2 (71% AA Identity, Homo sapiens)
SELEXJASPARInferred - Prrx2 (71% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Prrx2 (71% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - PRRX2 (71% AA Identity, Sus scrofa)
TransfacTransfacLicense requiredInferred - VSX2 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - PRRX2 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - VSX2 (71% AA Identity, Homo sapiens)
B1HJASPARInferred - al (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - al (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - ALX1 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX1 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx1 (70% AA Identity, Mus musculus)
PBMBerger08Inferred - Alx1 (70% AA Identity, Mus musculus)
B1HJASPARInferred - CG11294 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG32532 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32532 (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (70% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - CRX (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - CRX (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - CRX (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Crx (70% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - PHOX2A (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2A (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2a (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - PHOX2B (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - PHOX2B (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2B (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2b (70% AA Identity, Mus musculus)
PBMBerger08Inferred - Prrx1 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - VSX1 (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - VSX1 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Vsx1 (70% AA Identity, Mus musculus)
PBMZoo_01Inferred - vsx2 (70% AA Identity, Danio rerio)
TransfacTransfacLicense requiredInferred - ALX1 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CRX (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - CRX (70% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Crx (70% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - PRRX1 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Prrx1 (70% AA Identity, Rattus norvegicus)
MiscHocoMocoInferred - ALX1 (70% AA Identity, Homo sapiens)
MiscHocoMocoInferred - CRX (70% AA Identity, Homo sapiens)
MiscHOMERInferred - Crx (70% AA Identity, Mus musculus)
MiscHOMERInferred - Phox2a (70% AA Identity, Mus musculus)
MiscHocoMocoInferred - PRRX1 (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ISX (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ISX (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ISX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ISX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - PHOX2B (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - UNCX (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - UNCX (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Uncx (68% AA Identity, Mus musculus)
PBMZoo_01Inferred - uncx4.1 (68% AA Identity, Tetraodon nigroviridis)
PBMBarrera2016Inferred - VSX1 (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ESX1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ESX1 (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ISX (66% AA Identity, Homo sapiens)
B1HJASPARInferred - PHDP (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - PHDP (66% AA Identity, Drosophila melanogaster)
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)
PBMBarrera2016Inferred - CRX (65% 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