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    HOXA1 homeobox A1 [ Homo sapiens (human) ]

    Gene ID: 3198, updated on 7-Apr-2024

    Summary

    Official Symbol
    HOXA1provided by HGNC
    Official Full Name
    homeobox A1provided by HGNC
    Primary source
    HGNC:HGNC:5099
    See related
    Ensembl:ENSG00000105991 MIM:142955; AllianceGenome:HGNC:5099
    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
    BSAS; HOX1; HOX1F
    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. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms containing the homeodomain region. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in urinary bladder (RPKM 4.0), skin (RPKM 1.0) and 13 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See HOXA1 in Genome Data Viewer
    Location:
    7p15.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (27092993..27096000, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (27228895..27231899, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (27132612..27135619, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene tropomyosin 3 pseudogene 4 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:27069907-27070612 Neighboring gene NHP2 ribonucleoprotein pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:27131207-27132117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27133706-27134206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27134207-27134707 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

    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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat specifically associates with HOXA1 promoter to upregulate HOXA1 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

    Clone Names

    • MGC45232

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in abducens nerve formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in anatomical structure morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in artery development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in artery morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cochlea development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cochlea morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cognition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in embryonic neurocranium morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in inner ear development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuromuscular process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in optokinetic behavior IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in outer ear morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of behavior IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in semicircular canal formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    homeobox protein Hox-A1
    Names
    HOX A1 homeodomain protein
    Hox 1.6-like protein
    homeo box A1
    homeobox 1F
    homeobox protein Hox-1F
    lab-like protein

    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.

    Genomic

    1. NG_011813.2 RefSeqGene

      Range
      5000..8007
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005522.5NP_005513.2  homeobox protein Hox-A1 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5401.1
      UniProtKB/Swiss-Prot
      A4D184, B2R8U7, O43363, P49639
      UniProtKB/TrEMBL
      A0A2R8Y4R9
      Related
      ENSP00000494260.2, ENST00000643460.2
      Conserved Domains (2) summary
      COG5576
      Location:176286
      COG5576; Homeodomain-containing transcription factor [Transcription]
      pfam00046
      Location:233286
      Homeobox; Homeobox domain
    2. NM_153620.3NP_705873.3  homeobox protein Hox-A1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5402.2
      UniProtKB/TrEMBL
      A4D185, E7ERT8
      Related
      ENSP00000347851.5, ENST00000355633.5

    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
      27092993..27096000 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      27228895..27231899 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)