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HOXA4 homeobox A4 [ Homo sapiens (human) ]

Gene ID: 3201, updated on 17-Jun-2024


Official Symbol
HOXA4provided by HGNC
Official Full Name
homeobox A4provided by HGNC
Primary source
See related
Ensembl:ENSG00000197576 MIM:142953; AllianceGenome:HGNC:5105
Gene type
protein coding
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
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. [provided by RefSeq, Jul 2008]
Broad expression in esophagus (RPKM 4.4), lung (RPKM 4.1) and 19 other tissues See more
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Genomic context

See HOXA4 in Genome Data Viewer
Exon count:
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (27128525..27130757, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (27264506..27266738, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (27168144..27170376, 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 homeobox A3 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 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27179129-27179707 Neighboring gene HOXA cluster antisense RNA 3 Neighboring gene homeobox A5 Neighboring gene homeobox A6

Genomic regions, transcripts, and products


  • 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


GeneRIFs: Gene References Into Functions

What's a GeneRIF?


EBI GWAS Catalog

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

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat specifically associates with HOXA4 promoter to upregulate HOXA4 expression in T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem


Products Interactant Other Gene Complex Source Pubs Description

General gene information


Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
involved_in anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
involved_in embryonic skeletal system morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
located_in nuclear body IDA
Inferred from Direct Assay
more info
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info

General protein information

Preferred Names
homeobox protein Hox-A4
Dfd-like protein
Hox-1.4-like protein
homeo box A4
homeobox protein Hox-1.4
homeobox protein Hox-1D

NCBI Reference Sequences (RefSeq)

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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_002141.5NP_002132.3  homeobox protein Hox-A4

    See identical proteins and their annotated locations for NP_002132.3

    Status: REVIEWED

    Source sequence(s)
    AC004080, AW445008, M74297
    Consensus CDS
    A4D180, O43366, Q00056
    ENSP00000353151.5, ENST00000360046.10
    Conserved Domains (1) summary
    Homeobox; Homeobox domain

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


  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    27128525..27130757 complement
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0


  1. NC_060931.1 Alternate T2T-CHM13v2.0

    27264506..27266738 complement
    GenBank, FASTA, Sequence Viewer (Graphics)