Format

Send to:

Choose Destination

HOXD3 homeobox D3 [ Homo sapiens (human) ]

Gene ID: 3232, updated on 13-Mar-2020

Summary

Official Symbol
HOXD3provided by HGNC
Official Full Name
homeobox D3provided by HGNC
Primary source
HGNC:HGNC:5137
See related
Ensembl:ENSG00000128652 MIM:142980
Gene type
protein coding
RefSeq status
VALIDATED
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

Genomic context

See HOXD3 in Genome Data Viewer
Location:
2q31.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (176157307..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

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

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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, 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
 
nuclear chromatin ISA
Inferred from Sequence Alignment
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 

General protein information

Preferred Names
homeobox protein Hox-D3
Names
Hox-4.1, mouse, homolog of
homeo box D3
homeobox protein Hox-4A

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.

mRNA and Protein(s)

  1. NM_006898.5NP_008829.3  homeobox protein Hox-D3

    See identical proteins and their annotated locations for NP_008829.3

    Status: VALIDATED

    Source sequence(s)
    AC009336
    Consensus CDS
    CCDS2270.1
    UniProtKB/Swiss-Prot
    P31249
    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 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
    176157307..176173102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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
    Related
    ENSP00000249440.2, ENST00000249440.4
    Conserved Domains (2) summary
    pfam00046
    Location:198250
    Homeobox; Homeobox domain
    pfam13293
    Location:369430
    DUF4074; Domain of unknown function (DUF4074)
  2. 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)
  3. 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, ENST00000410016.5
    Conserved Domains (2) summary
    pfam00046
    Location:198250
    Homeobox; Homeobox domain
    pfam13293
    Location:369430
    DUF4074; Domain of unknown function (DUF4074)
  4. 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)
Support Center