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 ... See more...

Aliases for HOXD3 Gene

Aliases for HOXD3 Gene

  • Homeobox D3 2 3 5
  • Homeobox Protein Hox-D3 3 4
  • Homeobox Protein Hox-4A 3 4
  • Homeo Box D3 2 3
  • HOX1D 3 4
  • HOX4A 3 4
  • Hox-4.1, Mouse, Homolog Of 3
  • Hox-4.1 3
  • HOXD3 5
  • 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. Diseases associated with HOXD3 include Duane Retraction Syndrome. 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HOXD3 Gene

Genomics for HOXD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HOXD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J176128 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 -1.8 -1822 13.3 EZH2 ZNF654 MYC ZNF600 IKZF1 ZNF580 CEBPA ZSCAN16 NFIC ZIC2 HOXD4 HOXD8 HOXD-AS2 HOXD3 LOC401021 HOXD1 HAGLR HOXD9 HAGLROS HOXD11
GH02J176171 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 261.3 +35.1 35146 0.9 SIN3A YY1 RBM22 ZNF792 EGR1 SP1 ZNF143 USF2 USF1 RBFOX2 HOXD3 HAGLROS HAGLR HOXD-AS2 HOXD10 HOXD11 HOXD8 HOXD12 HOXD9 HOXD13
GH02J176176 Promoter 0.6 EPDnew 261.3 +35.7 35745 0.1 RBM22 ZNF792 GATA4 EZH2 POLR2A RBFOX2 HOXD3 HOXD-AS2 HOXD10 HOXD11 HOXD8 HOXD12 HOXD9 HOXD13 HAGLROS ENSG00000272729
GH02J176162 Promoter 0.5 EPDnew 261.5 +26.3 26324 0.1 CBX8 EZH2 HOXD3 HAGLR HOXD1 HOXD-AS2 HOXD9 HOXD8 HOXD10 HOXD11 HOXD13 ENSG00000272729
GH02J176173 Promoter 0.4 EPDnew 261.3 +34.5 34504 0.1 EZH2 HOXD3 HOXD-AS2 HOXD10 HOXD11 HOXD8 HOXD12 HOXD9 HOXD13 HAGLROS ENSG00000272729
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HOXD3

Top Transcription factor binding sites by QIAGEN in the HOXD3 gene promoter:
  • c-Ets-1
  • COMP1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • FOXO1a
  • HOXA5

Genomic Locations for HOXD3 Gene

Latest Assembly
chr2:176,136,612-176,173,102
(GRCh38/hg38)
Size:
36,491 bases
Orientation:
Plus strand

Previous Assembly
chr2:177,022,035-177,037,826
(GRCh37/hg19 by Entrez Gene)
Size:
15,792 bases
Orientation:
Plus strand

chr2:177,001,340-177,037,830
(GRCh37/hg19 by Ensembl)
Size:
36,491 bases
Orientation:
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:
    P31249-HXD3_HUMAN
    Recommended name:
    Homeobox protein Hox-D3
    Protein Accession:
    P31249
    Secondary Accessions:
    • Q99955
    • Q9BSC5

    Protein attributes for HOXD3 Gene

    Size:
    432 amino acids
    Molecular mass:
    45730 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • 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

Other Protein References for HOXD3 Gene

Antibodies for research

  • Abcam antibodies for HOXD3
  • Boster Bio Antibodies for HOXD3
  • Santa Cruz Biotechnology (SCBT) Antibodies for HOXD3

No data available for DME Specific Peptides for HOXD3 Gene

Domains & Families for HOXD3 Gene

Gene Families for HOXD3 Gene

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

Protein Domains for HOXD3 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
  • Homeobox protein, antennapedia type

Suggested Antigen Peptide Sequences for HOXD3 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein Hox-4A (HXD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P31249

UniProtKB/Swiss-Prot:

HXD3_HUMAN :
  • Belongs to the Antp homeobox family.
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

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

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:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 14610084
GO:0003677 DNA binding IEA --
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:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXD3

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

COMPARTMENTS
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
plasma membrane 2
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IBA,IC 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

SIGNOR curated interactions for HOXD3 Gene

Activates:
Is activated by:

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:0006357 regulation of transcription by RNA polymerase II IBA 21873635
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

Drugs & Compounds for HOXD3 Gene

No Compound Related Data Available

Transcripts for HOXD3 Gene

mRNA/cDNA for HOXD3 Gene

1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXD3

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

No ASD Table

Relevant External Links for HOXD3 Gene

GeneLoc Exon Structure for
HOXD3

Expression for HOXD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HOXD3

SOURCE GeneReport for Unigene cluster for HOXD3 Gene:

Hs.93574

Evidence on tissue expression from TISSUES for HOXD3 Gene

  • Nervous system(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with HOXD3: view

Primer products for research

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
Chimpanzee
(Pan troglodytes)
Mammalia HOXD3 29 30
  • 97.92 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia HOXD3 29 30
  • 92.73 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia HOXD3 29 30
  • 91.98 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Hoxd3 29
  • 90.9 (n)
Mouse
(Mus musculus)
Mammalia Hoxd3 29 16 30
  • 90.12 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia HOXD3 30
  • 81 (a)
OneToOne
Chicken
(Gallus gallus)
Aves HOXD3 29 30
  • 76.38 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia HOXD3 30
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hoxd3 29
  • 68.61 (n)
Zebrafish
(Danio rerio)
Actinopterygii hoxd3a 29 30
  • 65.74 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 17 (a)
OneToMany
Species where no ortholog for HOXD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for HOXD3 (if available)
TreeFam:
Gene Tree for HOXD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HOXD3: view image
Alliance of Genome Resources:
Additional Orthologs for HOXD3

Paralogs for HOXD3 Gene

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

  • HXD3_HUMAN
  • C9J1M3_HUMAN
  • L8E8D1_HUMAN
genes like me logo Genes that share paralogs with HOXD3: view

Variants for HOXD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HOXD3 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs141168805 Benign: not provided 176,169,267(+) A/C
NM_006898.5(HOXD3):c.153A>C (p.Pro51=)
SYNONYMOUS
rs1051932 -- p.Ser129Cys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HOXD3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
HOXD3
Leiden Open Variation Database (LOVD)
HOXD3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD3 Gene

Disorders for HOXD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HOXD3 Gene - From: GCD

Disorder Aliases PubMed IDs
duane retraction syndrome
  • duane's syndrome
- elite association - COSMIC cancer census association via MalaCards
Search HOXD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HOXD3

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with HOXD3: view

No data available for 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 40
  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 40
  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 40
  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
  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

Products for HOXD3 Gene

Sources for HOXD3 Gene