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HOXA3 homeobox A3 [ Homo sapiens (human) ]

Gene ID: 3200, updated on 13-Mar-2020

Summary

Official Symbol
HOXA3provided by HGNC
Official Full Name
homeobox A3provided by HGNC
Primary source
HGNC:HGNC:5104
See related
Ensembl:ENSG00000105997 MIM:142954
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

Genomic context

See HOXA3 in Genome Data Viewer
Location:
7p15.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (27106190..27153238, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (27145803..27179805, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2148 Neighboring gene HOXA transcript antisense RNA, myeloid-specific 1 Neighboring gene homeobox A2 Neighboring gene HOXA cluster antisense RNA 2 Neighboring gene homeobox A4 Neighboring gene HOXA cluster antisense RNA 3 Neighboring gene homeobox A5 Neighboring gene homeobox A6 Neighboring gene homeobox A7 Neighboring gene HOXA10-HOXA9 readthrough Neighboring gene NUP98-HOXA9 recombination region Neighboring gene homeobox A9

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC10155

Gene Ontology Provided by GOA

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

General protein information

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)

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_030661.4NP_109377.1  homeobox protein Hox-A3 isoform a

    See identical proteins and their annotated locations for NP_109377.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1 and 2 both encode isoform a.
    Source sequence(s)
    AC004079, BC015180
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33
    Related
    ENSP00000379640.3, ENST00000396352.8
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)
  2. NM_153631.2NP_705895.1  homeobox protein Hox-A3 isoform a

    See identical proteins and their annotated locations for NP_705895.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode isoform a.
    Source sequence(s)
    AC004079, AK056567, AK094200
    Consensus CDS
    CCDS5404.1
    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33, A4D182, B3KPN8
    Related
    ENSP00000484411.1, ENST00000612286.4
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    27106190..27153238 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011515343.3XP_011513645.1  homeobox protein Hox-A3 isoform X1

    See identical proteins and their annotated locations for XP_011513645.1

    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)
  2. XM_005249730.2XP_005249787.1  homeobox protein Hox-A3 isoform X1

    See identical proteins and their annotated locations for XP_005249787.1

    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33
    Related
    ENSP00000324884.2, ENST00000317201.6
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)
  3. XM_006715715.2XP_006715778.1  homeobox protein Hox-A3 isoform X1

    See identical proteins and their annotated locations for XP_006715778.1

    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)
  4. XM_005249732.4XP_005249789.1  homeobox protein Hox-A3 isoform X1

    See identical proteins and their annotated locations for XP_005249789.1

    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)
  5. XM_005249731.2XP_005249788.1  homeobox protein Hox-A3 isoform X1

    See identical proteins and their annotated locations for XP_005249788.1

    UniProtKB/Swiss-Prot
    O43365
    UniProtKB/TrEMBL
    A0A024RA33
    Conserved Domains (2) summary
    pfam00046
    Location:195247
    Homeobox; Homeobox domain
    pfam13293
    Location:377441
    DUF4074; Domain of unknown function (DUF4074)

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.
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