TF Info Page for HOXA3 (Homeodomain)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer 100 perc ID - in vitro

Description

Description: homeobox A3 [Source:HGNC Symbol;Acc:HGNC:5104]
Entrez Summary In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000105997
External Link: CisBP
Interpro IPR001356; IPR001827; IPR009057; IPR017970; IPR020479; IPR025281;
Protein Domain: ENSP00000379640
Protein Domain: ENSP00000484411
Protein Domain: ENSP00000429426
Protein Domain: ENSP00000430566
Domain:
Protein: ENSP00000379640DBD: HomeodomainOther: DUF4074
Protein: ENSP00000484411DBD: HomeodomainOther: DUF4074
Protein: ENSP00000429426DBD: HomeodomainOther:
Protein: ENSP00000430566DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:8096059 15914537
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 GO:0003700
sequence-specific DNA binding transcription factor activity
IEA - GO_REF:0000002
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
TransfacTransfacLicense requiredDirect
PBMBadis09Inferred - Hoxa3 (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa3 (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxb3 (98% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD3 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (98% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd3 (98% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - PDX1 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PDX1 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PDX1 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Pdx1 (78% AA Identity, Mus musculus)
SELEXJASPARInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (78% AA Identity, Homo sapiens)
MiscHocoMocoInferred - PDX1 (78% AA Identity, Homo sapiens)
MiscHOMERInferred - Pdx1 (78% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA2 (77% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (77% AA Identity, Homo sapiens)
PBMZoo_01Inferred - HOXA2 (77% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa2 (77% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA5 (77% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (77% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa5 (77% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (77% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB5 (77% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (77% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb5 (77% AA Identity, Mus musculus)
PBMZoo_01Inferred - SPU_026099 (77% AA Identity, Strongylocentrotus purpuratus)
COMPILEDJASPARInferred - HOXA5 (77% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA5 (77% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxa2 (77% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXA5 (77% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb4 (75% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxc5 (75% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD4 (75% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (75% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Q0N4M8_NEMVE (75% AA Identity, Nematostella vectensis)
B1HJASPARInferred - Scr (75% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Scr (75% AA Identity, Drosophila melanogaster)
MiscHOMERInferred - Hoxb4 (75% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXD4 (75% AA Identity, Homo sapiens)
B1HJASPARInferred - Antp (73% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Dfd (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (73% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA4 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa4 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA6 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa6 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA7 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa7 (73% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa7 (73% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXC4 (73% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc4 (73% AA Identity, Mus musculus)
B1HJASPARInferred - pb (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - pb (73% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Antp (73% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Dfd (73% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA4 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA7 (73% AA Identity, Homo sapiens)
MisciDMMPMMInferred - Antp (73% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - Dfd (73% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXA7 (73% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb7 (71% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXC4 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc6 (71% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXB7 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXC6 (71% AA Identity, Homo sapiens)
B1HJASPARInferred - abd-A (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - ftz (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - ftz (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXB6 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb6 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXB7 (70% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (70% AA Identity, Homo sapiens)
PBMBusserDevelopment2012Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Ubx (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Ubx (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - zen (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen (70% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - abd-A (70% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ftz (70% AA Identity, Drosophila melanogaster)
ChIP-seqmodENCODEInferred - lin-39 (70% AA Identity, Caenorhabditis elegans)
TransfacTransfacLicense requiredInferred - Ubx (70% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - abd-A (70% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - ftz (70% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXB6 (70% AA Identity, Homo sapiens)
MiscHOMERInferred - lin-39 (70% AA Identity, Caenorhabditis elegans)
MisciDMMPMMInferred - Ubx (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA9 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA9 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa9 (68% AA Identity, Mus musculus)
B1HJASPARInferred - lab (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - lab (68% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - NEMVEDRAFT_v1g205636 (68% AA Identity, Nematostella vectensis)
PBMZoo_01Inferred - Q24782_9CNID (68% AA Identity, Eleutheria dichotoma)
B1HJASPARInferred - zen2 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA9 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (68% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Hoxa9 (68% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXA9 (68% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA9 (68% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxa9 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - GSX1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - GSX1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - GSX2 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - GSX2 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Gsx2 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA1 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa1 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB1 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB9 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb9 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc9 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
B1HJASPARInferred - ind (66% AA Identity, Drosophila melanogaster)
ChIP-seqJASPARInferred - Hoxc9 (66% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXD9 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA1 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXB1 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxc9 (66% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXD9 (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