TF Info Page for HOXD4 (Homeodomain)

Conclusion

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

Description

Description: homeobox D4 [Source:HGNC Symbol;Acc:HGNC:5138]
Entrez Summary This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in determining positional values in developing limb buds. Alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000170166
External Link: CisBP
Interpro IPR001356; IPR001827; IPR009057; IPR017970; IPR017995; IPR020479;
Protein Domain: ENSP00000302548
Domain:
Protein: ENSP00000302548DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:1756725
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
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
MiscHocoMocoDirect
HT-SELEXYin2017Inferred - HOXA4 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA4 (98% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa4 (98% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXA4 (98% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXC4 (96% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (96% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc4 (96% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (94% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb4 (94% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXC4 (94% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxb4 (94% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA5 (92% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (92% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa5 (92% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB5 (92% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (92% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb5 (92% AA Identity, Mus musculus)
COMPILEDJASPARInferred - HOXA5 (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA5 (92% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA5 (92% AA Identity, Homo sapiens)
B1HJASPARInferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Dfd (91% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - Dfd (91% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Hoxc5 (89% AA Identity, Mus musculus)
B1HJASPARInferred - Scr (89% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Scr (89% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Antp (87% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (87% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa7 (87% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa7 (87% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXB7 (87% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb7 (87% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Antp (87% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA7 (87% AA Identity, Homo sapiens)
MisciDMMPMMInferred - Antp (87% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXA7 (87% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXB7 (87% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (85% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (85% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (84% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa6 (84% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (84% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (84% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb6 (84% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXB6 (84% AA Identity, Homo sapiens)
B1HJASPARInferred - abd-A (82% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (82% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Hoxc6 (82% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - abd-A (82% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - abd-A (82% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXC6 (82% AA Identity, Homo sapiens)
B1HJASPARInferred - ftz (80% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - ftz (80% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ftz (80% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - ftz (80% AA Identity, Drosophila melanogaster)
PBMBusserDevelopment2012Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Ubx (78% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
ChIP-seqmodENCODEInferred - lin-39 (78% AA Identity, Caenorhabditis elegans)
TransfacTransfacLicense requiredInferred - Ubx (78% AA Identity, Drosophila melanogaster)
MiscHOMERInferred - lin-39 (78% AA Identity, Caenorhabditis elegans)
MisciDMMPMMInferred - Ubx (78% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Hoxb3 (77% AA Identity, Mus musculus)
PBMZoo_01Inferred - SPU_026099 (77% AA Identity, Strongylocentrotus purpuratus)
PBMBadis09Inferred - Hoxa3 (75% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa3 (75% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (75% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd3 (75% AA Identity, Mus musculus)
PBMZoo_01Inferred - Q0N4M8_NEMVE (75% AA Identity, Nematostella vectensis)
TransfacTransfacLicense requiredInferred - HOXA3 (75% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd8 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - PDX1 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PDX1 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PDX1 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Pdx1 (73% AA Identity, Mus musculus)
SELEXJASPARInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (73% AA Identity, Homo sapiens)
MiscHocoMocoInferred - PDX1 (73% AA Identity, Homo sapiens)
MiscHOMERInferred - Pdx1 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB8 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb8 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD8 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD8 (71% AA Identity, Homo sapiens)
B1HJASPARInferred - lab (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - lab (71% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - pb (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - pb (71% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXB8 (71% AA Identity, Homo sapiens)
PBMTF_EvolutionUnpublished DataInferred - Cbr-mab-5 (70% AA Identity, Caenorhabditis briggsae)
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)
HT-SELEXYin2017Inferred - HOXC8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC8 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc8 (70% AA Identity, Mus musculus)
B1HJASPARInferred - zen (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen (70% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXC8 (70% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxa2 (70% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXC8 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - GSX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - GSX1 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - GSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - GSX2 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Gsx2 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB9 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB9 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb9 (68% AA Identity, Mus musculus)
B1HJASPARInferred - ind (68% AA Identity, Drosophila melanogaster)
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)
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 - HOXA9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa9 (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 - 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)
PBMZoo_01Inferred - O76842_CUPSA (66% AA Identity, Cupiennius salei)
PBMZoo_01Inferred - Q7M3U4_ACRFO (66% AA Identity, Acropora formosa)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Hoxa9 (66% AA Identity, Mus musculus)
ChIP-seqJASPARInferred - Hoxc9 (66% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXD9 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA1 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA9 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA9 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxa9 (66% AA Identity, Mus musculus)
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