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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. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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

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

Genomics for HOXD3 Gene

Regulatory Elements for HOXD3 Gene

Enhancers for HOXD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G176552 1.5 FANTOM5 Ensembl ENCODE 11.4 +417.1 417079 3.0 ARNT FEZF1 ZNF2 ZBTB7B YY1 ZNF143 REST ZNF592 ATF4 SMARCA4 HOXD4 HOXD3 HOXD-AS2 MIR10B HOXD1 HAGLR HOXD13 ENSG00000236231 GC02P176590
GH02G176177 1.1 Ensembl ENCODE 11.5 +41.8 41806 2.2 PKNOX1 FEZF1 GLIS2 ZNF366 FOS EGR2 SP3 ZNF114 ZNF579 PRDM6 HAGLROS HAGLR HOXD1 HOXD4 HOXD3 HOXD-AS2 MIR10B HOXD11 HOXD12 HOXD10
GH02G176489 1.2 Ensembl ENCODE 10.5 +354.4 354388 2.5 PKNOX1 FOXA2 SIN3A FEZF1 TCF12 FOS JUNB TBX21 SMARCA4 GLIS1 HAGLR HOXD1 HOXD3 ENSG00000229434 ENSG00000237260
GH02G176653 1 FANTOM5 ENCODE 11.5 +517.5 517488 0.2 ZNF263 CTCF ZNF654 TEAD1 TRIM22 SIN3A RAD21 GATA3 FOXK2 ZNF341 HOXD3 HOXD8 HOXD-AS2 HOXD9 HOXD11 LINC01116 GC02P176666 GC02P176638
GH02G176581 1.1 Ensembl ENCODE 10.3 +446.6 446597 3.3 INSM2 SIN3A KLF17 ZNF2 RAD21 GLIS2 GATA2 ZNF366 SCRT2 RCOR1 HOXD3 MIR10B HOXD4 GC02P176590 ENSG00000236231
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOXD3 on UCSC Golden Path with GeneCards custom track

Promoters for HOXD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000126751 88 1001 PKNOX1 ZSCAN4 ZNF76 FEZF1 GLI4 ZNF2 GLIS2 ZNF366 SCRT2 EGR2

Genomic Location for HOXD3 Gene

Chromosome:
2
Start:
176,136,612 bp from pter
End:
176,173,102 bp from pter
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

No data available for DME Specific Peptides for HOXD3 Gene

Domains & Families for HOXD3 Gene

Gene Families for HOXD3 Gene

Suggested Antigen Peptide Sequences for HOXD3 Gene

GenScript: Design optimal peptide antigens:

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

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.

Gene Ontology (GO) - Molecular Function for HOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
GO:0005515 protein binding IPI 23088713
GO:0043565 sequence-specific 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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

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
cytosol 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for HOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,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

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:0007160 cell-matrix adhesion IDA 7742539
GO:0007219 Notch signaling pathway IMP 12836255
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with HOXD3: view

No data available for SIGNOR curated interactions for HOXD3 Gene

Transcripts for HOXD3 Gene

Unigene Clusters for HOXD3 Gene

Homeobox D3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for HOXD3 Gene

GeneLoc Exon Structure for
HOXD3
ECgene alternative splicing isoforms for
HOXD3

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:

HOXD3

SOURCE GeneReport for Unigene cluster for HOXD3 Gene:

Hs.93574

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

Primer Products

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 34 35
  • 97.92 (n)
dog
(Canis familiaris)
Mammalia HOXD3 34 35
  • 92.73 (n)
cow
(Bos Taurus)
Mammalia HOXD3 34 35
  • 91.98 (n)
rat
(Rattus norvegicus)
Mammalia Hoxd3 34
  • 90.9 (n)
mouse
(Mus musculus)
Mammalia Hoxd3 34 16 35
  • 90.12 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HOXD3 35
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves HOXD3 34 35
  • 76.38 (n)
lizard
(Anolis carolinensis)
Reptilia HOXD3 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd3 34
  • 68.61 (n)
zebrafish
(Danio rerio)
Actinopterygii hoxd3a 34 35
  • 65.74 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 17 (a)
OneToMany
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

ENSEMBL:
Gene Tree for HOXD3 (if available)
TreeFam:
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 Sequence Context AA Info Type
rs104893636 Uncertain significance 176,151,875(+) ACAAG(A/C/T)GCCAG intron-variant, reference, missense
rs1000017558 -- 176,145,327(+) ACAGC(A/G)GCAGT intron-variant
rs1000060384 -- 176,143,027(+) CTCCT(A/T)GTACT intron-variant
rs1000159751 -- 176,157,150(+) CCGCG(C/T)CGGGC intron-variant, upstream-variant-2KB
rs1000251570 -- 176,170,273(+) CATAA(A/C)CATGA 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)

Relevant External Links for HOXD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXD3

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

Disorders for HOXD3 Gene

Relevant External Links for HOXD3

Genetic Association Database (GAD)
HOXD3
Human Genome Epidemiology (HuGE) Navigator
HOXD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOXD3

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 E.L. … Pharoah P.D. (Nat. Genet. 2010) 3 46 64
  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 L.M. … Zmuda J.M. (J. Bone Miner. Res. 2009) 3 46 64
  3. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester A.R. … Hecht J.T. (Am. J. Med. Genet. A 2009) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  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 64

Products for HOXD3 Gene

Sources for HOXD3 Gene

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