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Aliases for HOXD3 Gene

Aliases for HOXD3 Gene

  • Homeobox D3 2 3 5
  • Homeobox Protein Hox-4A 3 4
  • Homeo Box D3 2 3
  • HOX1D 3 4
  • HOX4A 3 4
  • Hox-4.1, Mouse, Homolog Of 3
  • Homeobox Protein Hox-D3 3
  • Hox-4.1 3
  • HOX4 3

External Ids for HOXD3 Gene

Previous HGNC Symbols for HOXD3 Gene

  • HOX4A
  • HOX4
  • HOX1D

Previous GeneCards Identifiers for HOXD3 Gene

  • GC02P175081
  • GC02P175689
  • GC02P176992
  • GC02P177231
  • GC02P176854
  • GC02P176737
  • GC02P177001
  • GC02P168905

Summaries for HOXD3 Gene

Entrez Gene Summary for HOXD3 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 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 the regulation of cell adhesion processes. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD3 Gene

HOXD3 (Homeobox D3) 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 DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is HOXB3.

UniProtKB/Swiss-Prot for HOXD3 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 HOXD3 Gene

Additional gene information for HOXD3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD3 Gene

Genomics for HOXD3 Gene

GeneHancer (GH) Regulatory Elements for HOXD3 Gene

Promoters and enhancers for HOXD3 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
GH02I176128 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 550.8 -1.8 -1822 13.3 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ZNF213 E2F8 HOXD8 HOXD3 HOXD1 HAGLR ATF2 HOXD4 HOXD9 HAGLROS HOXD11 HOXD-AS2
GH02I176552 Enhancer 1.3 FANTOM5 Ensembl ENCODE 11.4 +417.1 417079 3 ARNT FEZF1 ZNF2 ZBTB7B YY1 ZNF280A E2F8 ZNF143 ATF7 RUNX3 HNRNPA3 HOXD4 HOXD3 HOXD-AS2 MIR10B HAGLR HOXD1 HOXD13 ENSG00000236231 GC02P176590
GH02I176489 Enhancer 1.1 Ensembl ENCODE 10.5 +354.4 354387 2.5 PKNOX1 FEZF1 BATF TCF12 EGR1 ATF7 FOS BCLAF1 IKZF2 RUNX3 HAGLR HOXD1 HOXD3 ENSG00000229434 PPIAP67
GH02I176653 Enhancer 0.9 FANTOM5 ENCODE 11.6 +517.5 517487 0.2 CTCF ZNF654 TEAD1 TRIM22 RAD21 ZNF148 GATA3 FOXK2 ZNF341 ZNF143 HOXD3 HOXD8 HOXD-AS2 HOXD9 HOXD11 LINC01116 GC02P176666 GC02P176638 LINC01117
GH02I176177 Enhancer 0.9 Ensembl ENCODE 11.5 +41.8 41806 2.2 CTCF USF1 ZNF777 SUZ12 JUN MAX E2F1 ZFHX2 CTBP1 EGR2 HAGLROS HAGLR HOXD1 HOXD4 HOXD3 HOXD-AS2 MIR10B HOXD11 HOXD12 HOXD10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HOXD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXD3 gene promoter:

Genomic Locations for HOXD3 Gene

Genomic Locations for HOXD3 Gene
36,491 bases
Plus strand

Genomic View for HOXD3 Gene

Genes around HOXD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD3 Gene

Proteins for HOXD3 Gene

  • Protein details for HOXD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-D3
    Protein Accession:
    Secondary Accessions:
    • Q99955
    • Q9BSC5

    Protein attributes for HOXD3 Gene

    432 amino acids
    Molecular mass:
    45730 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA01891.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for HOXD3 Gene

Post-translational modifications for HOXD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HOXD3 Gene

Domains & Families for HOXD3 Gene

Gene Families for HOXD3 Gene

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

Suggested Antigen Peptide Sequences for HOXD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Antp homeobox family.
  • Belongs to the Antp homeobox family.
genes like me logo Genes that share domains with HOXD3: view

Function for HOXD3 Gene

Molecular function for HOXD3 Gene

GENATLAS Biochemistry:
homeo box D3(4A),homologous to mouse Hox-4.1,Drosophila Zen
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 HOXD3 Gene

Gene Ontology (GO) - Molecular Function for HOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 7913891
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI 23088713
genes like me logo Genes that share ontologies with HOXD3: view
genes like me logo Genes that share phenotypes with HOXD3: view

Animal Models for HOXD3 Gene

MGI Knock Outs for HOXD3:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD3 Gene

Localization for HOXD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD3 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 HOXD3 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IC,IEA 12836255
GO:0005654 nucleoplasm IDA --
GO:0016235 aggresome IDA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with HOXD3: view

Pathways & Interactions for HOXD3 Gene

genes like me logo Genes that share pathways with HOXD3: view

Gene Ontology (GO) - Biological Process for HOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IMP 12836255
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0007160 cell-matrix adhesion IDA 7742539
GO:0007219 Notch signaling pathway IMP 12836255
genes like me logo Genes that share ontologies with HOXD3: view

No data available for SIGNOR curated interactions for HOXD3 Gene

Drugs & Compounds for HOXD3 Gene

No Compound Related Data Available

Transcripts for HOXD3 Gene

Unigene Clusters for HOXD3 Gene

Homeobox D3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD3 Gene

No ASD Table

Relevant External Links for HOXD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD3 Gene

This gene is overexpressed in Uterus (x6.8), Kidney - Cortex (x5.7), and Ovary (x4.4).

NURSA nuclear receptor signaling pathways regulating expression of HOXD3 Gene:


SOURCE GeneReport for Unigene cluster for HOXD3 Gene:


Evidence on tissue expression from TISSUES for HOXD3 Gene

  • Lung(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with HOXD3: 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 HOXD3 Gene

Orthologs for HOXD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXD3 33 34
  • 97.92 (n)
(Canis familiaris)
Mammalia HOXD3 33 34
  • 92.73 (n)
(Bos Taurus)
Mammalia HOXD3 33 34
  • 91.98 (n)
(Rattus norvegicus)
Mammalia Hoxd3 33
  • 90.9 (n)
(Mus musculus)
Mammalia Hoxd3 33 16 34
  • 90.12 (n)
(Ornithorhynchus anatinus)
Mammalia HOXD3 34
  • 81 (a)
(Gallus gallus)
Aves HOXD3 33 34
  • 76.38 (n)
(Anolis carolinensis)
Reptilia HOXD3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd3 33
  • 68.61 (n)
(Danio rerio)
Actinopterygii hoxd3a 33 34
  • 65.74 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 17 (a)
Species where no ortholog for HOXD3 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)
  • oppossum (Monodelphis domestica)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for HOXD3 Gene

Gene Tree for HOXD3 (if available)
Gene Tree for HOXD3 (if available)

Paralogs for HOXD3 Gene

Paralogs for HOXD3 Gene

(4) SIMAP similar genes for HOXD3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with HOXD3: view

Variants for HOXD3 Gene

Sequence variations from dbSNP and Humsavar for HOXD3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs104893636 uncertain-significance, Leukemia, acute lymphoblastic, susceptibility to 176,151,875(+) A/C/T genic_upstream_transcript_variant, intron_variant
rs1000017558 -- 176,145,327(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000060384 -- 176,143,027(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000159751 -- 176,157,150(+) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000251570 -- 176,170,273(+) C/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXD3 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV gain 20364138
nsv953525 CNV deletion 24416366

Variation tolerance for HOXD3 Gene

Residual Variation Intolerance Score: 34% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.92; 35.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXD3 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 HOXD3 Gene

Disorders for HOXD3 Gene

Additional Disease Information for HOXD3

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

No disorders were found for HOXD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXD3 Gene

Publications for HOXD3 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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Overexpression of the HOX4A (HOXD3) homeobox gene in human erythroleukemia HEL cells results in altered adhesive properties. (PMID: 7742539) Taniguchi Y … Moriuchi T (Blood 1995) 3 22 58

Products for HOXD3 Gene

Sources for HOXD3 Gene

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