TF Info Page for HOXA1 (Homeodomain)

Conclusion

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

Description

Description: Homeobox A1 [Source:HGNC Symbol;Acc:HGNC:5099]
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. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms containing the homeodomain region. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000105991
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000343246
Protein Domain: ENSP00000347851
Domain:
Protein: ENSP00000343246DBD: HomeodomainOther:
Protein: ENSP00000347851DBD: 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. 		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
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
MiscHocoMocoDirect
PBMBerger08Inferred - Hoxa1 (100% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB1 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB1 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB1 (87% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd1 (87% AA Identity, Mus musculus)
B1HJASPARInferred - lab (87% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - lab (87% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - O76842_CUPSA (87% AA Identity, Cupiennius salei)
MiscHocoMocoInferred - HOXB1 (87% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD1 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD1 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD1 (85% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA2 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (70% AA Identity, Homo sapiens)
PBMZoo_01Inferred - HOXA2 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa2 (70% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (70% AA Identity, Homo sapiens)
B1HJASPARInferred - pb (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - pb (70% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Q24782_9CNID (70% AA Identity, Eleutheria dichotoma)
PBMZoo_01Inferred - Q7M3U4_ACRFO (70% AA Identity, Acropora formosa)
MiscHOMERInferred - Hoxa2 (70% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA4 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA4 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa4 (68% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxc5 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD3 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd3 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXA4 (68% AA Identity, Homo sapiens)
PBMBadis09Inferred - Hoxa3 (66% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa3 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA5 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa5 (66% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxb3 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb4 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB5 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb5 (66% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXC4 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc4 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD4 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (66% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Q0N4M8_NEMVE (66% AA Identity, Nematostella vectensis)
B1HJASPARInferred - Scr (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Scr (66% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA3 (66% AA Identity, Homo sapiens)
COMPILEDJASPARInferred - HOXA5 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA5 (66% AA Identity, Homo sapiens)
ChIP-seqmodENCODEInferred - lin-39 (66% AA Identity, Caenorhabditis elegans)
MiscHocoMocoInferred - HOXA5 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxb4 (66% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXD4 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - lin-39 (66% AA Identity, Caenorhabditis elegans)

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