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Aliases for HOXD11 Gene

Aliases for HOXD11 Gene

  • Homeobox D11 2 3 5
  • Homeobox Protein Hox-4F 3 4
  • Homeo Box D11 2 3
  • HOX4F 3 4
  • Hox-4.6, Mouse, Homolog Of 3
  • Homeobox Protein Hox-D11 3
  • Homeo Box 4F 3
  • HOX4 3

External Ids for HOXD11 Gene

Previous HGNC Symbols for HOXD11 Gene

  • HOX4
  • HOX4F

Previous GeneCards Identifiers for HOXD11 Gene

  • GC02P175024
  • GC02P175633
  • GC02P176936
  • GC02P177174
  • GC02P176797
  • GC02P176680
  • GC02P168849

Summaries for HOXD11 Gene

Entrez Gene Summary for HOXD11 Gene

  • 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]

GeneCards Summary for HOXD11 Gene

HOXD11 (Homeobox D11) is a Protein Coding gene. Diseases associated with HOXD11 include Syndactyly, Type V and Synpolydactyly. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXA11.

UniProtKB/Swiss-Prot for HOXD11 Gene

  • Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Gene Wiki entry for HOXD11 Gene

Additional gene information for HOXD11 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD11 Gene

Genomics for HOXD11 Gene

GeneHancer (GH) Regulatory Elements for HOXD11 Gene

Promoters and enhancers for HOXD11 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I176107 Promoter 1.1 EPDnew 550.8 +3.0 3045 0.1 PKNOX1 ARNT INSM2 KLF17 MZF1 SIN3A FEZF1 GLIS2 ZNF391 USF2 HOXD10 HOXD11
GH02I176105 Enhancer 1 FANTOM5 569.7 +1.1 1135 0.4 INSM2 KLF17 ZNF76 FEZF1 ZEB1 ZNF335 GLIS2 ZNF213 ZNF366 KLF7 HOXD11 HOXD13 HOXD10 HOXD9 HOXD8 HOXD3
GH02I176128 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 10.7 +30.6 30574 13.3 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ZNF213 E2F8 HOXD8 HOXD3 HOXD1 HAGLR ATF2 HOXD4 HOXD9 HAGLROS HOXD11 HOXD-AS2
GH02I176073 Enhancer 0.8 UCNEbase 11.4 -30.5 -30505 0.5 PKNOX1 HLF ZBTB8A FOXA1 ZNF664 OSR2 PRDM6 EZH2 HOXD11 HOXD12 HOXD10 HOXD1 HAGLR LNPK EVX2 GC02M176020
GH02I176455 Enhancer 0.9 Ensembl ENCODE 10 +351.7 351673 1.8 CTCF RB1 BMI1 ZSCAN9 RAD21 ZFHX2 POLR2A SMC3 ZNF143 RCOR1 HOXD4 MIR10B HOXD3 HOXD11 HOXD10 ENSG00000229434 PPIAP67
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HOXD11 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXD11 gene promoter:

Genomic Locations for HOXD11 Gene

Genomic Locations for HOXD11 Gene
5,539 bases
Plus strand

Genomic View for HOXD11 Gene

Genes around HOXD11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD11 Gene

Proteins for HOXD11 Gene

  • Protein details for HOXD11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-D11
    Protein Accession:
    Secondary Accessions:
    • A6NIS4
    • Q9NS02

    Protein attributes for HOXD11 Gene

    338 amino acids
    Molecular mass:
    35197 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXD11 Gene

Post-translational modifications for HOXD11 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXD11 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD11 Gene

Domains & Families for HOXD11 Gene

Gene Families for HOXD11 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for HOXD11 Gene

Suggested Antigen Peptide Sequences for HOXD11 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Abd-B homeobox family.
  • Belongs to the Abd-B homeobox family.
genes like me logo Genes that share domains with HOXD11: view

Function for HOXD11 Gene

Molecular function for HOXD11 Gene

GENATLAS Biochemistry:
homeo box D11(4F),homologous to mouse Hox-4.6
UniProtKB/Swiss-Prot Function:
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Phenotypes From GWAS Catalog for HOXD11 Gene

Gene Ontology (GO) - Molecular Function for HOXD11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXD11: view
genes like me logo Genes that share phenotypes with HOXD11: view

Animal Models for HOXD11 Gene

MGI Knock Outs for HOXD11:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD11 Gene

Localization for HOXD11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD11 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOXD11 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXD11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with HOXD11: view

Pathways & Interactions for HOXD11 Gene

SuperPathways for HOXD11 Gene

No Data Available

SIGNOR curated interactions for HOXD11 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HOXD11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001658 branching involved in ureteric bud morphogenesis ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0009953 dorsal/ventral pattern formation ISS --
genes like me logo Genes that share ontologies with HOXD11: view

No data available for Pathways by source for HOXD11 Gene

Drugs & Compounds for HOXD11 Gene

No Compound Related Data Available

Transcripts for HOXD11 Gene

mRNA/cDNA for HOXD11 Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(56) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOXD11 Gene

Homeobox D11:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD11 Gene

No ASD Table

Relevant External Links for HOXD11 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXD11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXD11 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD11 Gene

This gene is overexpressed in Uterus (x13.3), Vagina (x9.7), Colon - Sigmoid (x9.5), Prostate (x5.8), Cervix - Ectocervix (x5.2), and Kidney - Cortex (x4.0).

Protein differential expression in normal tissues from HIPED for HOXD11 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HOXD11 Gene

Protein tissue co-expression partners for HOXD11 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXD11 Gene:


SOURCE GeneReport for Unigene cluster for HOXD11 Gene:


Evidence on tissue expression from TISSUES for HOXD11 Gene

  • Kidney(2.5)
  • Stomach(2.5)
  • Muscle(2.2)
  • Nervous system(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with HOXD11: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXD11 Gene

Orthologs for HOXD11 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXD11 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXD11 33 34
  • 96.25 (n)
(Canis familiaris)
Mammalia HOXD11 34
  • 96 (a)
(Bos Taurus)
Mammalia HOXD 34
  • 95 (a)
HOXD11 33
  • 91.37 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 88 (a)
(Mus musculus)
Mammalia Hoxd11 33 16 34
  • 87.2 (n)
(Monodelphis domestica)
Mammalia HOXD11 34
  • 83 (a)
(Gallus gallus)
Aves HOXD11 33 34
  • 72.5 (n)
(Anolis carolinensis)
Reptilia HOXD11 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd11 33
  • 65.33 (n)
(Danio rerio)
Actinopterygii hoxd11a 33 34
  • 58.91 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 12 (a)
Species where no ortholog for HOXD11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HOXD11 Gene

Gene Tree for HOXD11 (if available)
Gene Tree for HOXD11 (if available)

Paralogs for HOXD11 Gene

(13) SIMAP similar genes for HOXD11 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HOXD11: view

Variants for HOXD11 Gene

Sequence variations from dbSNP and Humsavar for HOXD11 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000374466 -- 176,108,138(+) T/G splice_donor_variant
rs1000419816 -- 176,108,730(+) C/T intron_variant
rs1000580695 -- 176,109,113(+) C/G coding_sequence_variant, missense_variant
rs1001720766 -- 176,109,059(+) A/C coding_sequence_variant, missense_variant
rs1001926822 -- 176,108,306(+) G/A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXD11 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV gain 20364138
dgv7173n54 CNV loss 21841781
nsv1072996 CNV deletion 25765185
nsv1112777 CNV deletion 24896259
nsv1126572 CNV deletion 24896259
nsv517968 CNV loss 19592680
nsv520227 CNV loss 19592680
nsv524250 CNV loss 19592680
nsv527187 CNV loss 19592680
nsv583673 CNV loss 21841781

Variation tolerance for HOXD11 Gene

Gene Damage Index Score: 1.42; 27.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXD11 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD11 Gene

Disorders for HOXD11 Gene

MalaCards: The human disease database

(5) MalaCards diseases for HOXD11 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
syndactyly, type v
  • sdty5
  • syndactyly type 2
brachydactyly-syndactyly syndrome
  • bdsd
fraser syndrome 1
  • frasrs1
chromosome 2q35 duplication syndrome
  • syndactyly, type i; sdty1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HOXD11

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXD11: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOXD11 Gene

Publications for HOXD11 Gene

  1. Study of HOXD genes in autism particularly regarding the ratio of second to fourth digit length. (PMID: 19540081) Sugie Y … Osawa J (Brain & development 2010) 3 44 58
  2. Absence of mutations in the HOXA11 and HOXD11 genes in children with congenital renal malformations. (PMID: 19255789) Bouba I … Georgiou I (Pediatric nephrology (Berlin, Germany) 2009) 3 44 58
  3. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 44 58
  4. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester AR … Hecht JT (American journal of medical genetics. Part A 2009) 3 44 58
  5. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. (PMID: 17236141) Zhao X … Zhang X (American journal of human genetics 2007) 3 4 58

Products for HOXD11 Gene

Sources for HOXD11 Gene

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