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 g... See more...

Aliases for HOXA3 Gene

Aliases for HOXA3 Gene

  • Homeobox A3 2 3 5
  • Homeobox Protein Hox-A3 3 4
  • Homeobox Protein Hox-1E 3 4
  • Homeo Box A3 2 3
  • HOX1E 3 4
  • Hox-1.5-Like Protein 3
  • Homeo Box 1E 3
  • HOXA3 5
  • 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. Diseases associated with HOXA3 include Penile Cancer and Penile Benign Neoplasm. 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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HOXA3 Gene

Genomics for HOXA3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HOXA3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXA3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HOXA3

Top Transcription factor binding sites by QIAGEN in the HOXA3 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • HNF-4alpha1
  • HNF-4alpha2
  • Sp1

Genomic Locations for HOXA3 Gene

Latest Assembly
chr7:27,106,184-27,152,583
(GRCh38/hg38)
Size:
46,400 bases
Orientation:
Minus strand

Previous Assembly
chr7:27,146,629-27,192,202
(GRCh37/hg19 by Entrez Gene)
Size:
45,574 bases
Orientation:
Minus strand

chr7:27,145,803-27,192,200
(GRCh37/hg19 by Ensembl)
Size:
46,398 bases
Orientation:
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:
    O43365-HXA3_HUMAN
    Recommended name:
    Homeobox protein Hox-A3
    Protein Accession:
    O43365
    Secondary Accessions:
    • A4D181

    Protein attributes for HOXA3 Gene

    Size:
    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

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

Protein Domains for HOXA3 Gene

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

Suggested Antigen Peptide Sequences for HOXA3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ36881 fis, clone BGGI12001247, highly similar to HOMEOBOX PROTEIN HOX-A3 (A4D182_HUMAN)
  • Homeobox protein Hox-1E (HXA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43365

UniProtKB/Swiss-Prot:

HXA3_HUMAN :
  • Belongs to the Antp homeobox family.
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

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 A3(1E),homologous to mouse Hox-1.5,Drosophila Zen1,Zen2

Phenotypes From GWAS Catalog for HOXA3 Gene

Gene Ontology (GO) - Molecular Function for HOXA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
GO:0005515 protein binding IPI 21516116
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:

Transcription Factor Targets for HOXA3 Gene

Selected GeneGlobe predicted Target genes for HOXA3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA3

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

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 HOXA3 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
cytosol 1

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:0000785 chromatin ISA --
GO:0005634 nucleus IBA 21873635
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:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
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

mRNA/cDNA for HOXA3 Gene

15 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
7 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 HOXA3

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

No ASD Table

Relevant External Links for HOXA3 Gene

GeneLoc Exon Structure for
HOXA3

Expression for HOXA3 Gene

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



Protein tissue co-expression partners for HOXA3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HOXA3

SOURCE GeneReport for Unigene cluster for HOXA3 Gene:

Hs.659337

Evidence on tissue expression from TISSUES for HOXA3 Gene

  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with HOXA3: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt 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
Chimpanzee
(Pan troglodytes)
Mammalia HOXA3 29 30
  • 99.62 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia HOXA3 29 30
  • 90.25 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Hoxa3 29 16 30
  • 88.84 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Hoxa3 29
  • 88.49 (n)
Cow
(Bos Taurus)
Mammalia HOXA3 29 30
  • 88.08 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia HOXA3 30
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia HOXA3 30
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves HOXA3 29 30 30
  • 76.27 (n)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia HOXA3 30
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hoxa3 29
  • 70.62 (n)
African clawed frog
(Xenopus laevis)
Amphibia hoxa3a-prov 29
Zebrafish
(Danio rerio)
Actinopterygii hoxa3a 29 30
  • 63.43 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 19 (a)
OneToMany
Species where no ortholog for HOXA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 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 HOXA3 Gene

ENSEMBL:
Gene Tree for HOXA3 (if available)
TreeFam:
Gene Tree for HOXA3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HOXA3: view image
Alliance of Genome Resources:
Additional Orthologs for HOXA3

Paralogs for HOXA3 Gene

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

  • HXA3_HUMAN
  • A4D182_HUMAN
  • E5RGW8_HUMAN
  • E5RIJ8_HUMAN
  • F2Z3A4_HUMAN
genes like me logo Genes that share paralogs with HOXA3: view

Variants for HOXA3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HOXA3 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs149964084 Benign: not provided 27,143,527(-) A/G
NM_019102.4(HOXA5):c.81T>C (p.His27=)
SYNONYMOUS
rs764656757 A breast cancer sample p.Asp42Asn
VAR_036265 A breast cancer sample p.Ala131Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HOXA3 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 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
HOXA3
Leiden Open Variation Database (LOVD)
HOXA3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA3 Gene

Disorders for HOXA3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for HOXA3 Gene - From: COP

Disorder Aliases PubMed IDs
penile cancer
  • ca penis
penile benign neoplasm
  • neoplasm of penis
congenital aphakia
  • aphakia, congenital primary
hand-foot-genital syndrome
  • hfg
ectopic thymus
- elite association - COSMIC cancer census association via MalaCards
Search HOXA3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HOXA3

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 HOXA3: view

No data available for 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 40
  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
  3. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4
  4. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4
  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

Products for HOXA3 Gene

Sources for HOXA3 Gene