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    HOXD9 homeobox D9 [ Homo sapiens (human) ]

    Gene ID: 3235, updated on 18-Sep-2024

    Summary

    Official Symbol
    HOXD9provided by HGNC
    Official Full Name
    homeobox D9provided by HGNC
    Primary source
    HGNC:HGNC:5140
    See related
    Ensembl:ENSG00000128709 MIM:142982; AllianceGenome:HGNC:5140
    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
    HOX4; HOX4C; Hox-4.3; Hox-5.2
    Summary
    This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The exact role of this gene has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in endometrium (RPKM 16.0), kidney (RPKM 11.1) and 10 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HOXD9 in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (176122719..176124937)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (176610853..176613074)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (176987447..176989665)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene homeobox D11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176980400-176981072 Neighboring gene homeobox D10 Neighboring gene uncharacterized LOC100129455 Neighboring gene homeobox D8 Neighboring gene HOXD cluster antisense RNA 2 Neighboring gene uncharacterized LOC401021

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-02-22)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-02-22)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in adult locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic skeletal system morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mammary gland development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in peripheral nervous system neuron development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proximal/distal pattern formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in single fertilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skeletal muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    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

    Preferred Names
    homeobox protein Hox-D9
    Names
    Hox-4.3, mouse, homolog of
    homeo box D9
    homeobox protein Hox-4C
    homeobox protein Hox-5.2

    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_009225.1 RefSeqGene

      Range
      5035..7253
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014213.4NP_055028.3  homeobox protein Hox-D9

      See identical proteins and their annotated locations for NP_055028.3

      Status: REVIEWED

      Source sequence(s)
      AC009336, BC044855, BU732638, X59372
      Consensus CDS
      CCDS2267.2
      UniProtKB/Swiss-Prot
      P28356, Q86ST1
      Related
      ENSP00000249499.6, ENST00000249499.8
      Conserved Domains (2) summary
      smart00389
      Location:285337
      HOX; Homeodomain
      pfam04617
      Location:11164
      Hox9_act; Hox9 activation region

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      176122719..176124937
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      176610853..176613074
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)