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Aliases for HOXA3 Gene

Aliases for HOXA3 Gene

  • Homeobox A3 2 3 5
  • Homeobox Protein Hox-1E 3 4
  • Homeo Box A3 2 3
  • HOX1E 3 4
  • Homeobox Protein Hox-A3 3
  • Hox-1.5-Like Protein 3
  • Homeo Box 1E 3
  • HOX1 3

External Ids for HOXA3 Gene

Previous HGNC Symbols for HOXA3 Gene

  • HOX1E
  • HOX1

Previous GeneCards Identifiers for HOXA3 Gene

  • GC07M026788
  • GC07M026888
  • GC07M026919
  • GC07M027113
  • GC07M027026

Summaries for HOXA3 Gene

Entrez Gene Summary for HOXA3 Gene

  • In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXA3 Gene

HOXA3 (Homeobox A3) 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 HMG box domain binding. An important paralog of this gene is HOXB3.

UniProtKB/Swiss-Prot for HOXA3 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 HOXA3 Gene

Additional gene information for HOXA3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXA3 Gene

Genomics for HOXA3 Gene

GeneHancer (GH) Regulatory Elements for HOXA3 Gene

Promoters and enhancers for HOXA3 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
GH07I027095 Promoter/Enhancer 3.4 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 561 +14.4 14386 86.3 MLX FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC SSRP1 ZNF610 HOXA2 HOXA9 HOXA10 HOXA1 HOXA3 HOXA6 HOXA4 HOXA5 HOXA7 HNRNPA2B1
GH07I026195 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 10.3 +951.8 951813 10.1 CLOCK FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC GLIS1 HNRNPA2B1 CBX3 HOXA3 ENSG00000273237 GC07M026184
GH07I027661 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.3 -510.3 -510322 3.3 HNRNPUL1 PKNOX1 CLOCK FOXA2 SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 HIBADH EIF4HP1 HOXA7 HOXA3 LOC105375211
GH07I026855 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.2 +295.0 295033 4.8 HDAC1 PKNOX1 FEZF1 ZBTB40 TCF12 GLIS2 EGR1 ZNF366 EGR2 ZNF362 HOTAIRM1 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1 HOXA2 HOXA-AS2 SKAP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HOXA3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXA3 gene promoter:

Genomic Locations for HOXA3 Gene

Genomic Locations for HOXA3 Gene
46,398 bases
Minus strand

Genomic View for HOXA3 Gene

Genes around HOXA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXA3 Gene

Proteins for HOXA3 Gene

  • Protein details for HOXA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-A3
    Protein Accession:
    Secondary Accessions:
    • A4D181

    Protein attributes for HOXA3 Gene

    443 amino acids
    Molecular mass:
    46369 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXA3 Gene

Post-translational modifications for HOXA3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HOXA3 Gene

Domains & Families for HOXA3 Gene

Gene Families for HOXA3 Gene

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

Suggested Antigen Peptide Sequences for HOXA3 Gene

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 HOXA3: view

Function for HOXA3 Gene

Molecular function for HOXA3 Gene

GENATLAS Biochemistry:
homeo box A3(1E),homologous to mouse Hox-1.5,Drosophila Zen1,Zen2
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 HOXA3 Gene

Gene Ontology (GO) - Molecular Function for HOXA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI 21516116
GO:0043565 sequence-specific DNA binding IEA --
GO:0071837 HMG box domain binding IEA --
genes like me logo Genes that share ontologies with HOXA3: view
genes like me logo Genes that share phenotypes with HOXA3: view

Animal Models for HOXA3 Gene

MGI Knock Outs for HOXA3:

Animal Model Products

Transcription Factor Targets for HOXA3 Gene

Selected GeneGlobe predicted Target genes for HOXA3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for HOXA3 Gene

Localization for HOXA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA3 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 HOXA3 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXA3 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 HOXA3: view

Pathways & Interactions for HOXA3 Gene

genes like me logo Genes that share pathways with HOXA3: view

Gene Ontology (GO) - Biological Process for HOXA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEP 17972163
GO:0001974 blood vessel remodeling IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with HOXA3: view

No data available for SIGNOR curated interactions for HOXA3 Gene

Drugs & Compounds for HOXA3 Gene

(1) Additional Compounds for HOXA3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HOXA3: view

Transcripts for HOXA3 Gene

Unigene Clusters for HOXA3 Gene

Homeobox A3:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA3 Gene

No ASD Table

Relevant External Links for HOXA3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXA3 Gene

mRNA differential expression in normal tissues according to GTEx for HOXA3 Gene

This gene is overexpressed in Fallopian Tube (x4.3).

Protein differential expression in normal tissues from HIPED for HOXA3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HOXA3 Gene

Protein tissue co-expression partners for HOXA3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HOXA3 Gene:


SOURCE GeneReport for Unigene cluster for HOXA3 Gene:

genes like me logo Genes that share expression patterns with HOXA3: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA3 Gene

Orthologs for HOXA3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXA3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXA3 33 34
  • 99.62 (n)
(Canis familiaris)
Mammalia HOXA3 33 34
  • 90.25 (n)
(Mus musculus)
Mammalia Hoxa3 33 16 34
  • 88.84 (n)
(Rattus norvegicus)
Mammalia Hoxa3 33
  • 88.49 (n)
(Bos Taurus)
Mammalia HOXA3 33 34
  • 88.08 (n)
(Monodelphis domestica)
Mammalia HOXA3 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia HOXA3 34
  • 70 (a)
(Gallus gallus)
Aves HOXA3 33 34 34
  • 76.27 (n)
(Anolis carolinensis)
Reptilia HOXA3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxa3 33
  • 70.62 (n)
African clawed frog
(Xenopus laevis)
Amphibia hoxa3a-prov 33
(Danio rerio)
Actinopterygii hoxa3a 33 34
  • 63.43 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 19 (a)
Species where no ortholog for HOXA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 HOXA3 Gene

Gene Tree for HOXA3 (if available)
Gene Tree for HOXA3 (if available)

Paralogs for HOXA3 Gene

Paralogs for HOXA3 Gene

(5) SIMAP similar genes for HOXA3 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with HOXA3: view

Variants for HOXA3 Gene

Sequence variations from dbSNP and Humsavar for HOXA3 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs764656757 A breast cancer sample 27,110,517(-) C/A/T coding_sequence_variant, missense_variant
VAR_036265 A breast cancer sample p.Ala131Thr
rs1000045615 -- 27,113,619(-) G/C intron_variant
rs1000079925 -- 27,150,131(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000231152 -- 27,116,735(-) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXA3 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
dgv11244n54 CNV loss 21841781
esv3444885 CNV insertion 20981092
esv3612654 CNV loss 21293372
nsv1076881 CNV deletion 25765185
nsv1126777 CNV deletion 24896259
nsv5674 CNV deletion 18451855
nsv606464 CNV loss 21841781
nsv606465 CNV loss 21841781
nsv7393 OTHER inversion 18451855

Variation tolerance for HOXA3 Gene

Residual Variation Intolerance Score: 25.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.94; 35.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXA3 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 HOXA3 Gene

Disorders for HOXA3 Gene

Additional Disease Information for HOXA3

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

No disorders were found for HOXA3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXA3 Gene

Publications for HOXA3 Gene

  1. 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
  2. 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
  3. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 58
  4. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4 58
  5. Krox20 and kreisler co-operate in the transcriptional control of segmental expression of Hoxb3 in the developing hindbrain. (PMID: 11823429) Manzanares M … Charnay P (The EMBO journal 2002) 3 22 58

Products for HOXA3 Gene

Sources for HOXA3 Gene

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