The Human Transcription Factors

Conclusion

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

Description

Description:

homeobox D11 [Source:HGNC Symbol;Acc:HGNC:5134]

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 in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. The product of the mouse Hoxd11 gene plays a role in forelimb morphogenesis. [provided by RefSeq, Jul 2008]

Ensembl ID:

ENSG00000128713

External Link:

CisBP

Interpro

IPR001356; IPR009057; IPR017970; IPR020479; IPR021918; ;

Protein Domain:

ENSP00000249504

Protein Domain:

ENSP00000480304

Domain:

Protein: ENSP00000249504	DBD: Homeodomain	Other: DUF3528
Protein: ENSP00000480304	DBD: Homeodomain	Other: DUF3528

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-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
PBM	Berger08		Inferred - Hoxd11 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA11 (98% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA11 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA11 (98% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA11 (98% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa11 (98% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC11 (96% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc11 (96% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA10 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa10 (71% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC10 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxc10 (71% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxd10 (71% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Hoxa10 (71% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - HOXD10 (71% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXD10 (71% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC9 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXC9 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC9 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXC9 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXD9 (70% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXD9 (70% AA Identity, Homo sapiens)
PBM	BusserDevelopment2012		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxa9 (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXB9 (68% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - HOXB9 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXB9 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxb9 (68% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Hoxc9 (68% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - HOXD12 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HOXD12 (68% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Hoxd12_CONSTRUCT (68% AA Identity, PBM CONSTRUCTS)
Transfac	Transfac	License required	Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HOXA9 (68% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Hoxa9 (68% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - Hoxc9 (68% AA Identity, Mus musculus)
Misc	iDMMPMM		Inferred - Abd-B (68% AA Identity, Drosophila melanogaster)
Misc	HocoMoco		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HOXA9 (68% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Hoxa9 (68% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Hoxc9 (68% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - HXD12_HETFR (66% AA Identity, Heterodontus francisci)

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

Name
Email
Comment
Reference

{"regions": [{"startStyle": "curved", "end": 323, "endStyle": "curved", "aliStart": 267, "text": "HD", "colour": "#228B22", "aliEnd": 323, "start": 267, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 323, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 267, "scoreName": "E-value", "accession": "PF00046.27", "start": 267, "score": 2.3e-20, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 323}}, {"startStyle": "straight", "end": 81, "endStyle": "jagged", "aliStart": 26, "text": "DUF3528", "colour": "#9999ff", "aliEnd": 77, "start": 26, "href": "http://pfam.xfam.org/family/PF12045.6", "type": "pfama", "display": "true", "metadata": {"end": 81, "description": "This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 185 to 298 amino acids in length. This protein is found associated with Pfam:PF00046.", "database": "PfamA", "aliStart": 26, "scoreName": "E-value", "accession": "PF12045.6", "start": 26, "score": 5e-42, "identifier": "Protein of unknown function (DUF3528)", "type": "DBD", "aliEnd": 77}}, {"startStyle": "jagged", "end": 195, "endStyle": "jagged", "aliStart": 117, "text": "DUF3528", "colour": "#9999ff", "aliEnd": 187, "start": 105, "href": "http://pfam.xfam.org/family/PF12045.6", "type": "pfama", "display": "true", "metadata": {"end": 195, "description": "This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 185 to 298 amino acids in length. This protein is found associated with Pfam:PF00046.", "database": "PfamA", "aliStart": 117, "scoreName": "E-value", "accession": "PF12045.6", "start": 105, "score": 5e-42, "identifier": "Protein of unknown function (DUF3528)", "type": "DBD", "aliEnd": 187}}], "length": 339}

{"regions": [{"startStyle": "curved", "end": 146, "endStyle": "curved", "aliStart": 90, "text": "HD", "colour": "#228B22", "aliEnd": 146, "start": 90, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 146, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 90, "scoreName": "E-value", "accession": "PF00046.27", "start": 90, "score": 6.3999999999999996e-21, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 146}}, {"startStyle": "straight", "end": 41, "endStyle": "jagged", "aliStart": 13, "text": "DUF3528", "colour": "#9999ff", "aliEnd": 39, "start": 13, "href": "http://pfam.xfam.org/family/PF12045.6", "type": "pfama", "display": "true", "metadata": {"end": 41, "description": "This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 185 to 298 amino acids in length. This protein is found associated with Pfam:PF00046.", "database": "PfamA", "aliStart": 13, "scoreName": "E-value", "accession": "PF12045.6", "start": 13, "score": 1e-07, "identifier": "Protein of unknown function (DUF3528)", "type": "DBD", "aliEnd": 39}}], "length": 162}

TF Info Page for HOXD11 (Homeodomain)