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HOXD13 homeobox D13 [ Homo sapiens (human) ]

Gene ID: 3239, updated on 25-Apr-2020

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

Genomic context

See HOXD13 in Genome Data Viewer
Location:
2q31.1
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (176087487..176095944)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (176957532..176960666)

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 (2012-02-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-02-23)

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

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.

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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