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    HOXD3 homeobox D3 [ Homo sapiens (human) ]

    Gene ID: 3232, updated on 23-May-2018
    Official Symbol
    HOXD3provided by HGNC
    Official Full Name
    homeobox D3provided by HGNC
    Primary source
    HGNC:HGNC:5137
    See related
    Ensembl:ENSG00000128652 MIM:142980; Vega:OTTHUMG00000187566
    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; HOX1D; HOX4A; Hox-4.1
    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 protein encoded by this gene may play a role in the regulation of cell adhesion processes. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 1.9), endometrium (RPKM 1.4) and 11 other tissues See more
    Orthologs
    See HOXD3 in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (176157163..176173102)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (177001669..177043737)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene HOXD cluster antisense RNA 2 Neighboring gene uncharacterized LOC401021 Neighboring gene microRNA 10b Neighboring gene homeobox D4 Neighboring gene HOXD antisense growth-associated long non-coding RNA Neighboring gene HAGLR opposite strand lncRNA Neighboring gene microRNA 7704 Neighboring gene homeobox D1

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
    NHGRI GWA Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC10470

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    Notch signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    anterior/posterior pattern specification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cartilage development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell-matrix adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    embryonic skeletal system morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    embryonic skeletal system morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    glossopharyngeal nerve morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    thyroid gland development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    aggresome IDA
    Inferred from Direct Assay
    more info
     
    nuclear body IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IC
    Inferred by Curator
    more info
    PubMed 
    Preferred Names
    homeobox protein Hox-D3
    Names
    Hox-4.1, mouse, homolog of
    homeo box D3
    homeobox protein Hox-4A

    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_006898.4NP_008829.3  homeobox protein Hox-D3

      See identical proteins and their annotated locations for NP_008829.3

      Status: REVIEWED

      Source sequence(s)
      BC005124
      Consensus CDS
      CCDS2270.1
      UniProtKB/Swiss-Prot
      P31249
      Related
      ENSP00000249440.2, OTTHUMP00000163342, ENST00000249440.4, OTTHUMT00000255699
      Conserved Domains (2) summary
      pfam00046
      Location:198250
      Homeobox; Homeobox domain
      pfam13293
      Location:369430
      DUF4074; Domain of unknown function (DUF4074)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

      Range
      176157163..176173102
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005246513.5XP_005246570.1  homeobox protein Hox-D3 isoform X1

      See identical proteins and their annotated locations for XP_005246570.1

      UniProtKB/Swiss-Prot
      P31249
      Conserved Domains (2) summary
      pfam00046
      Location:198250
      Homeobox; Homeobox domain
      pfam13293
      Location:369430
      DUF4074; Domain of unknown function (DUF4074)
    2. XM_011511066.3XP_011509368.1  homeobox protein Hox-D3 isoform X1

      See identical proteins and their annotated locations for XP_011509368.1

      UniProtKB/Swiss-Prot
      P31249
      Conserved Domains (2) summary
      pfam00046
      Location:198250
      Homeobox; Homeobox domain
      pfam13293
      Location:369430
      DUF4074; Domain of unknown function (DUF4074)
    3. XM_005246511.4XP_005246568.1  homeobox protein Hox-D3 isoform X1

      See identical proteins and their annotated locations for XP_005246568.1

      UniProtKB/Swiss-Prot
      P31249
      Conserved Domains (2) summary
      pfam00046
      Location:198250
      Homeobox; Homeobox domain
      pfam13293
      Location:369430
      DUF4074; Domain of unknown function (DUF4074)
    4. XM_005246509.4XP_005246566.1  homeobox protein Hox-D3 isoform X1

      See identical proteins and their annotated locations for XP_005246566.1

      UniProtKB/Swiss-Prot
      P31249
      Related
      ENSP00000386498.1, OTTHUMP00000205235, ENST00000410016.5
      Conserved Domains (2) summary
      pfam00046
      Location:198250
      Homeobox; Homeobox domain
      pfam13293
      Location:369430
      DUF4074; Domain of unknown function (DUF4074)
    5. XM_011511065.3XP_011509367.1  homeobox protein Hox-D3 isoform X1

      See identical proteins and their annotated locations for XP_011509367.1

      UniProtKB/Swiss-Prot
      P31249
      Conserved Domains (2) summary
      pfam00046
      Location:198250
      Homeobox; Homeobox domain
      pfam13293
      Location:369430
      DUF4074; Domain of unknown function (DUF4074)
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