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    HOXD13 homeobox D13 [ Homo sapiens (human) ]

    Gene ID: 3239, updated on 19-Jul-2021

    Summary

    Official Symbol
    HOXD13provided by HGNC
    Official Full Name
    homeobox D13provided by HGNC
    Primary source
    HGNC:HGNC:5136
    See related
    Ensembl:ENSG00000128714 MIM:142989
    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
    BDE; SPD; BDSD; SPD1; HOX4I
    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 in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in colon (RPKM 2.7), prostate (RPKM 2.6) and 1 other tissue See more
    Orthologs
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    Genomic context

    See HOXD13 in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (176087487..176095944)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (176957449..176960672)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene even-skipped homeobox 2 Neighboring gene NUP98-HOXD13 recombination region Neighboring gene homeobox D12 Neighboring gene sine oculis-binding protein homolog

    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

    Associated conditions

    Description Tests
    Brachydactyly type D
    MedGen: C0220664 OMIM: 113200 GeneReviews: Not available
    Compare labs
    Brachydactyly type E1
    MedGen: C1862102 OMIM: 113300 GeneReviews: Not available
    Compare labs
    Brachydactyly-syndactyly syndrome
    MedGen: C1853137 OMIM: 610713 GeneReviews: Not available
    Compare labs
    Syndactyly, type V
    MedGen: C1861348 OMIM: 186300 GeneReviews: Not available
    Compare labs
    Synpolydactyly 1
    MedGen: C2699746 OMIM: 186000 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-09-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-23)

    ClinGen Genome Curation PagePubMed

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in branch elongation of an epithelium IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digit morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic hindgut morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in male genitalia development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in morphogenesis of an epithelial fold IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in multicellular organism development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of branching involved in prostate gland morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in response to testosterone IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skeletal system development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    homeobox protein Hox-D13
    Names
    homeo box 4I
    homeo box D13
    homeobox protein Hox-4I
    synpolydactyly

    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.

    Genomic

    1. NG_008137.1 RefSeqGene

      Range
      4918..8141
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000523.4NP_000514.2  homeobox protein Hox-D13

      See identical proteins and their annotated locations for NP_000514.2

      Status: REVIEWED

      Source sequence(s)
      AC009336, BX100910
      Consensus CDS
      CCDS2264.2
      UniProtKB/Swiss-Prot
      P35453
      Related
      ENSP00000376322.3, ENST00000392539.4
      Conserved Domains (2) summary
      cd00086
      Location:277333
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam12284
      Location:39174
      HoxA13_N; Hox protein A13 N terminal

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      176087487..176095944
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011511068.2XP_011509370.1  homeobox protein Hox-D13 isoform X1

      Conserved Domains (1) summary
      pfam00046
      Location:260313
      Homeobox; Homeobox domain
    2. XM_011511069.2XP_011509371.1  homeobox protein Hox-D13 isoform X2

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