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Aliases for HOXD1 Gene

Aliases for HOXD1 Gene

  • Homeobox D1 2 3 5
  • Homeobox Protein Hox-GG 3 4
  • Homeo Box D1 2 3
  • HOX4G 3 4
  • HOX4 3 4
  • Homeobox Protein Hox-D1 3
  • Homeo Box 4G 3
  • Hox-4.7 3

External Ids for HOXD1 Gene

Previous HGNC Symbols for HOXD1 Gene

  • HOX4
  • HOX4G

Previous GeneCards Identifiers for HOXD1 Gene

  • GC02P175105
  • GC02P175714
  • GC02P177017
  • GC02P177255
  • GC02P176878
  • GC02P176761
  • GC02P177053
  • GC02P168930

Summaries for HOXD1 Gene

Entrez Gene Summary for HOXD1 Gene

  • This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD1 Gene

HOXD1 (Homeobox D1) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Developmental Biology. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXA1.

UniProtKB/Swiss-Prot for HOXD1 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. Acts on the anterior body structures.

Gene Wiki entry for HOXD1 Gene

Additional gene information for HOXD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD1 Gene

Genomics for HOXD1 Gene

GeneHancer (GH) Regulatory Elements for HOXD1 Gene

Promoters and enhancers for HOXD1 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
GH02J176186 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 663.9 -0.2 -244 2.9 FOXA2 ZFP64 SIN3A DMAP1 GLI4 ZNF2 ZNF48 GLIS2 KLF7 ZNF202 HOXD1 HAGLR MIR7704 HAGLROS
GH02J176128 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 21.9 -53.8 -53789 13.3 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 ZNF213 HOXD4 HOXD8 HOXD3 HOXD1 HAGLR HOXD9 HAGLROS HOXD11 ATF2 HOXD-AS2
GH02J176552 Enhancer 1.3 FANTOM5 Ensembl ENCODE 10.2 +365.1 365112 3 ARNT FEZF1 ZNF2 ZBTB7B YY1 ZNF280A E2F8 ZNF143 ATF7 RUNX3 HNRNPA3 HOXD4 HOXD3 HOXD-AS2 MIR10B HAGLR HOXD1 HOXD13 ENSG00000236231 GC02P176590
GH02J176489 Enhancer 1.1 Ensembl ENCODE 10.9 +302.4 302420 2.5 PKNOX1 FEZF1 TCF12 ATF7 FOS RUNX3 RXRA JUNB SMARCA4 GLIS1 HAGLR HOXD1 HOXD3 ENSG00000229434 PPIAP67
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXD1 gene promoter:
  • Arnt
  • AhR
  • FOXF2
  • AP-4
  • Sox5
  • POU2F1
  • POU2F1a
  • HNF-1

Genomic Locations for HOXD1 Gene

Genomic Locations for HOXD1 Gene
2,329 bases
Plus strand
2,382 bases
Plus strand

Genomic View for HOXD1 Gene

Genes around HOXD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD1 Gene

Proteins for HOXD1 Gene

  • Protein details for HOXD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-D1
    Protein Accession:
    Secondary Accessions:
    • B2RAB4

    Protein attributes for HOXD1 Gene

    328 amino acids
    Molecular mass:
    34093 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXD1 Gene

Post-translational modifications for HOXD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD1 Gene

Domains & Families for HOXD1 Gene

Gene Families for HOXD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for HOXD1 Gene

Suggested Antigen Peptide Sequences for HOXD1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Antp homeobox family. Labial subfamily.
  • Belongs to the Antp homeobox family. Labial subfamily.
genes like me logo Genes that share domains with HOXD1: view

Function for HOXD1 Gene

Molecular function for HOXD1 Gene

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. Acts on the anterior body structures.
GENATLAS Biochemistry:
homeo box D1(4G),homologous to mouse Hox-4.9,Drosophila lab

Phenotypes From GWAS Catalog for HOXD1 Gene

Gene Ontology (GO) - Molecular Function for HOXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXD1: view
genes like me logo Genes that share phenotypes with HOXD1: view

Animal Models for HOXD1 Gene

MGI Knock Outs for HOXD1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD1 Gene

Localization for HOXD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD1 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 HOXD1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXD1 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 HOXD1: view

Pathways & Interactions for HOXD1 Gene

genes like me logo Genes that share pathways with HOXD1: view

Gene Ontology (GO) - Biological Process for HOXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0019233 sensory perception of pain IEA --
genes like me logo Genes that share ontologies with HOXD1: view

No data available for SIGNOR curated interactions for HOXD1 Gene

Drugs & Compounds for HOXD1 Gene

No Compound Related Data Available

Transcripts for HOXD1 Gene

mRNA/cDNA for HOXD1 Gene

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

Unigene Clusters for HOXD1 Gene

Homeobox D1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3
SP2: -

Relevant External Links for HOXD1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x10.8), Brain - Substantia nigra (x5.4), and Kidney - Cortex (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of HOXD1 Gene:


SOURCE GeneReport for Unigene cluster for HOXD1 Gene:


Evidence on tissue expression from TISSUES for HOXD1 Gene

  • Nervous system(4.4)
  • Stomach(2.3)
genes like me logo Genes that share expression patterns with HOXD1: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXD1 Gene

Orthologs for HOXD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXD1 34 33
  • 97.87 (n)
(Bos Taurus)
Mammalia HOXD1 34 33
  • 85.71 (n)
(Rattus norvegicus)
Mammalia Hoxd1 33
  • 82.56 (n)
(Canis familiaris)
Mammalia HOXD1 34 33
  • 82.11 (n)
(Mus musculus)
Mammalia Hoxd1 16 34 33
  • 81.95 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 75 (a)
-- 34
  • 63 (a)
(Monodelphis domestica)
Mammalia HOXD1 34
  • 69 (a)
(Anolis carolinensis)
Reptilia HOXD1 34
  • 34 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd1 33
  • 59.59 (n)
(Danio rerio)
Actinopterygii hoxc1a 34
  • 29 (a)
fruit fly
(Drosophila melanogaster)
Insecta lab 34
  • 15 (a)
(Caenorhabditis elegans)
Secernentea ceh-13 34
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
Species where no ortholog for HOXD1 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)
  • 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)

Evolution for HOXD1 Gene

Gene Tree for HOXD1 (if available)
Gene Tree for HOXD1 (if available)
Evolutionary constrained regions (ECRs) for HOXD1: view image

Paralogs for HOXD1 Gene

Paralogs for HOXD1 Gene

(2) SIMAP similar genes for HOXD1 Gene using alignment to 3 proteins:

  • Q8IZ25_HUMAN
  • Q96CA4_HUMAN
genes like me logo Genes that share paralogs with HOXD1: view

Variants for HOXD1 Gene

Sequence variations from dbSNP and Humsavar for HOXD1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000423196 -- 176,191,128(+) C/T downstream_transcript_variant
rs1001160152 -- 176,189,462(+) G/T intron_variant
rs1002154023 -- 176,189,146(+) C/G coding_sequence_variant, stop_gained
rs1003114523 -- 176,187,941(+) C/T upstream_transcript_variant
rs1003160256 -- 176,188,311(+) G/A/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXD1 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV gain 20364138
nsv1001933 CNV gain 25217958

Variation tolerance for HOXD1 Gene

Residual Variation Intolerance Score: 48.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.92; 83.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD1 Gene

Disorders for HOXD1 Gene

Additional Disease Information for HOXD1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HOXD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXD1 Gene

Publications for HOXD1 Gene

  1. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. (PMID: 20852632) Goode EL … Ovarian Cancer Association Consortium (OCAC) (Nature genetics 2010) 3 44 58
  2. 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
  3. 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
  4. Isolation and characterization of the human homeobox gene HOX D1. (PMID: 11455954) Appukuttan B … Stout JT (Molecular biology reports 2000) 3 4 58
  5. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott MP (Cell 1992) 2 3 58

Products for HOXD1 Gene

Sources for HOXD1 Gene

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