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    HOXA4 homeobox A4 [ Homo sapiens (human) ]

    Gene ID: 3201, updated on 27-Nov-2024

    Summary

    Official Symbol
    HOXA4provided by HGNC
    Official Full Name
    homeobox A4provided by HGNC
    Primary source
    HGNC:HGNC:5105
    See related
    Ensembl:ENSG00000197576 MIM:142953; AllianceGenome:HGNC:5105
    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; HOX1D
    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. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in esophagus (RPKM 4.4), lung (RPKM 4.1) and 19 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See HOXA4 in Genome Data Viewer
    Location:
    7p15.2
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (27128525..27130757, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (27264506..27266738, complement)
    RS_2024_09 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

    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

    EBI GWAS Catalog

    Description
    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    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
    located_in 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
    Names
    Dfd-like protein
    Hox-1.4-like protein
    homeo box A4
    homeobox protein Hox-1.4
    homeobox protein Hox-1D

    NCBI Reference Sequences (RefSeq)

    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_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
      CCDS5405.1
      UniProtKB/Swiss-Prot
      A4D180, O43366, Q00056
      Related
      ENSP00000353151.5, ENST00000360046.10
      Conserved Domains (1) summary
      pfam00046
      Location:218271
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

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