U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

HOXA3 homeobox A3 [ Homo sapiens (human) ]

Gene ID: 3200, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
HOXA3provided by HGNC
Official Full Name
homeobox A3provided by HGNC
Primary source
HGNC:HGNC:5104
See related
Ensembl:ENSG00000105997 MIM:142954; AllianceGenome:HGNC:5104
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HOX1; HOX1E
Summary
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]
Expression
Broad expression in kidney (RPKM 1.8), fat (RPKM 1.4) and 17 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See HOXA3 in Genome Data Viewer
Location:
7p15.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (27107010..27152583, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (27242907..27288574, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (27146629..27192202, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2148 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27136009-27136581 Neighboring gene HOXA transcript antisense RNA, myeloid-specific 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27142137-27142976 Neighboring gene homeobox A2 Neighboring gene Sharpr-MPRA regulatory region 6231 Neighboring gene NANOG hESC enhancer GRCh37_chr7:27152731-27153232 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:27155135-27155350 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:27161315-27162514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27163690-27164487 Neighboring gene HOXA cluster antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18042 Neighboring gene homeobox A4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27179129-27179707 Neighboring gene HOXA cluster antisense RNA 3 Neighboring gene homeobox A5 Neighboring gene homeobox A6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27194138-27194722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27200121-27200806 Neighboring gene homeobox A7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27201681-27202180 Neighboring gene HOXA10-HOXA9 readthrough Neighboring gene NUP98-HOXA9 recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27203692-27204569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27204570-27205446 Neighboring gene homeobox A9

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Downregulation of HOXA3 in lung adenocarcinoma and its relevant molecular mechanism analysed by RT-qPCR, TCGA and in silico analysis. Gan BL, et al. Int J Oncol, 2018 Oct. PMID 30066858, Free PMC Article
  2. Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression. Yang R, et al. Neuro Oncol, 2023 Apr 6. PMID 36215227, Free PMC Article
  3. ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3. Liu G, et al. J Cell Mol Med, 2021 Apr. PMID 33683826, Free PMC Article
  4. miR‑338‑3p suppresses the malignancy of T‑cell lymphoblastic lymphoma by downregulating HOXA3. Wang L, et al. Mol Med Rep, 2019 Sep. PMID 31322185, Free PMC Article
  5. The histone chaperone NAP1L3 is required for haematopoietic stem cell maintenance and differentiation. Heshmati Y, et al. Sci Rep, 2018 Jul 25. PMID 30046127, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HOXA3 functions as the on-off switch to regulate the development of hESC-derived third pharyngeal pouch endoderm through EPHB2-mediated Wnt pathway.
    Title: HOXA3 functions as the on-off switch to regulate the development of hESC-derived third pharyngeal pouch endoderm through EPHB2-mediated Wnt pathway.
  2. Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression.
    Title: Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression.
  3. ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3.
    Title: ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3.
  4. Bioinformatics analysis of putative target mRNAs of miR3383p identified a direct binding site in the 3'untranslated of homeobox A3 (HOXA3).
    Title: miR‑338‑3p suppresses the malignancy of T‑cell lymphoblastic lymphoma by downregulating HOXA3.
  5. we demonstrate that HOXA3 and HOXA5 genes are markedly upregulated when NAP1L3 is suppressed in umbilical cord blood (UCB) haematopoietic stem cells (HSCs). Taken together, our findings establish an important role for NAP1L3 in haematopoietic stem cells homeostasis and haematopoietic differentiation.
    Title: The histone chaperone NAP1L3 is required for haematopoietic stem cell maintenance and differentiation.
  6. Study indicated that low HOXA3 expression may play a certain role in lung adenocarcinoma; however, its association with lung squamous cell carcinoma still requires further investigation.
    Title: Downregulation of HOXA3 in lung adenocarcinoma and its relevant molecular mechanism analysed by RT-qPCR, TCGA and in silico analysis.
  7. aim of this work was to search for mutations in thyroid developmental candidate genes HOXA3, HOXB3, HOXD3 and PITX2
    Title: The absence of mutations in homeobox candidate genes HOXA3, HOXB3, HOXD3 and PITX2 in familial and sporadic thyroid hemiagenesis.
  8. HOXA7, HOXB3, HOXA3, and HOXB13 expression levels changed during angiogenesis, sugessting these proteins might be involved in the angiogenesis of hMSCs.
    Title: HOX gene analysis of endothelial cell differentiation in human bone marrow-derived mesenchymal stem cells.
  9. Observational study of gene-disease association. (HuGE Navigator)
    Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC10155

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables HMG box domain binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in angiogenesis IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in animal organ formation IEA
Inferred from Electronic Annotation
more info
  
involved_in anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in blood vessel remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in cartilage development IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic skeletal system morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in glossopharyngeal nerve morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in parathyroid gland development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of stem cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in specification of animal organ position IEA
Inferred from Electronic Annotation
more info
  
involved_in stem cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in thymus development IEA
Inferred from Electronic Annotation
more info
  
involved_in thyroid gland development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

Go to the top of the page Help
Preferred Names
homeobox protein Hox-A3
Names
Hox-1.5-like protein
homeo box 1E
homeo box A3
homeobox protein Hox-1E

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001384335.1 → NP_001371264.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  2. NM_001384336.1 → NP_001371265.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  3. NM_001384337.1 → NP_001371266.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  4. NM_001384338.1 → NP_001371267.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  5. NM_001384339.1 → NP_001371268.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  6. NM_001384340.1 → NP_001371269.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Related
    ENSP00000324884.2, ENST00000317201.7
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  7. NM_001384341.1 → NP_001371270.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  8. NM_001384342.1 → NP_001371271.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  9. NM_001384343.1 → NP_001371272.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  10. NM_001384344.1 → NP_001371273.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  11. NM_001384345.1 → NP_001371274.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  12. NM_001384346.1 → NP_001371275.1  homeobox protein Hox-A3

    Status: REVIEWED

    Source sequence(s)
    AC004079
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  13. NM_030661.5 → NP_109377.1  homeobox protein Hox-A3

    See identical proteins and their annotated locations for NP_109377.1

    Status: REVIEWED

    Source sequence(s)
    AC004079
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Related
    ENSP00000379640.3, ENST00000396352.8
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

  14. NM_153631.3 → NP_705895.1  homeobox protein Hox-A3

    See identical proteins and their annotated locations for NP_705895.1

    Status: REVIEWED

    Source sequence(s)
    AC004079, AC004080, AC010990
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    A4D181, O43365
    UniProtKB/TrEMBL
    B3KPN8
    Related
    ENSP00000484411.1, ENST00000612286.5
    Conserved Domains (2) summary
    pfam00046
    Location:195 → 248
    Homeobox; Homeobox domain
    pfam13293
    Location:378 → 441
    DUF4074; Domain of unknown function (DUF4074)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    27107010..27152583 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    27242907..27288574 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_153632.2: Suppressed sequence

    Description
    NM_153632.2: This RefSeq was permanently suppressed because it represents a poorly supported variant with non-consensus splice sites.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43365.1 GenPept UniProtKB/Swiss-Prot:O43365

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous