TF Info Page for PHOX2B (Homeodomain)

Conclusion

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

Description

Description: paired like homeobox 2b [Source:HGNC Symbol;Acc:HGNC:9143]
Entrez Summary The DNA-associated protein encoded by this gene is a member of the paired family of homeobox proteins localized to the nucleus. The protein functions as a transcription factor involved in the development of several major noradrenergic neuron populations and the determination of neurotransmitter phenotype. The gene product is linked to enhancement of second messenger-mediated activation of the dopamine beta-hydroylase, c-fos promoters and several enhancers, including cyclic amp-response element and serum-response element. Expansion of a 20 amino acid polyalanine tract in this protein by 5-13 aa has been associated with congenital central hypoventilation syndrome. [provided by RefSeq, Jul 2016]
Ensembl ID: ENSG00000109132
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; ;
Protein Domain: ENSP00000226382
Domain:
Protein: ENSP00000226382DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:11752063 16280598
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:16144830
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
PBMBarrera2016Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
HT-SELEXYin2017Inferred - PHOX2A (100% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PHOX2A (100% AA Identity, Homo sapiens)
PBMBerger08Inferred - Phox2a (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Phox2b (100% AA Identity, Mus musculus)
MiscHOMERInferred - Phox2a (100% AA Identity, Mus musculus)
B1HJASPARInferred - PHDP (84% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - PHDP (84% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - ARX (78% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ARX (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ARX (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Arx (78% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - DRGX (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - DRGX (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Arx (78% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - Drgx (78% AA Identity, Rattus norvegicus)
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)
HT-SELEXYin2017Inferred - ALX4 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX4 (77% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx4 (77% AA Identity, Mus musculus)
PBMBarrera2016Inferred - ARX (77% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (77% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (77% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (77% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - ARX (77% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - CG2808 (77% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ALX1 (77% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ALX4 (77% AA Identity, Homo sapiens)
MiscHocoMocoInferred - ALX1 (77% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX3 (75% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ALX3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ALX3 (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Alx3 (75% AA Identity, Mus musculus)
PBMBerger08Inferred - Otp (75% AA Identity, Mus musculus)
B1HJASPARInferred - Pph13 (75% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Pph13 (75% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG9876 (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG9876 (73% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG11294 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG11294 (71% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG32532 (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32532 (71% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - CRX (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Prrx1 (71% AA Identity, Mus musculus)
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)
TransfacTransfacLicense requiredInferred - PRRX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Prrx1 (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)
MiscHocoMocoInferred - PRRX1 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - PRRX2 (71% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - CG5369 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG5369 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG5369 (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)
B1HJASPARInferred - hbn (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - hbn (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - otp (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - otp (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - otp (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - OTX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - OTX2 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Otx2 (70% AA Identity, Mus musculus)
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 - Rx (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Rx (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - SHOX (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SHOX (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - SHOX (70% AA Identity, Homo sapiens)
PBMZoo_01Inferred - SHOX (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Shox2 (70% AA Identity, Mus musculus)
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 - OTX2 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - OTX2 (70% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Rax (70% AA Identity, Rattus norvegicus)
TransfacTransfacLicense requiredInferred - Shox2 (70% AA Identity, Rattus norvegicus)
MiscHocoMocoInferred - CRX (70% AA Identity, Homo sapiens)
MiscHOMERInferred - Crx (70% AA Identity, Mus musculus)
MiscHocoMocoInferred - OTX2 (70% AA Identity, Homo sapiens)
MiscHOMERInferred - Otx2 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - CRX (68% AA Identity, Homo sapiens)
B1HJASPARInferred - oc (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - oc (68% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - OdsH (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - OdsH (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - OdsH (68% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - OTX1 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - OTX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - OTX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - OTX1 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Otx1 (68% AA Identity, Mus musculus)
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 - VSX2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - VSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - VSX2 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - OTX1 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - VSX2 (68% AA Identity, Homo sapiens)
MisciDMMPMMInferred - oc (68% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - OTX1 (68% AA Identity, Homo sapiens)
MiscHocoMocoInferred - VSX2 (68% AA Identity, Homo sapiens)
PBMZoo_01Inferred - ENSCING00000016045 (66% AA Identity, Ciona intestinalis)
PBMBerger08Inferred - Isx (66% AA Identity, Mus musculus)
PBMZoo_01Inferred - Sebox (66% AA Identity, Mus musculus)
PBMZoo_01Inferred - si:dkey-43p13.5 (66% AA Identity, Danio rerio)
B1HJASPARInferred - unc-4 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - unc-4 (66% AA Identity, Drosophila melanogaster)
PBMBarrera2016Inferred - VSX1 (66% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - VSX1 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Vsx1 (66% AA Identity, Mus musculus)
PBMZoo_01Inferred - vsx2 (66% AA Identity, Danio rerio)
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