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HOXD9 homeobox D9 [ Homo sapiens (human) ]

Gene ID: 3235, updated on 11-Jun-2025
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
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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

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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
 
acts_upstream_of_or_within anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic skeletal system morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within embryonic skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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 
acts_upstream_of_or_within peripheral nervous system neuron development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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
 
acts_upstream_of_or_within proximal/distal pattern formation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of gene expression 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
 
acts_upstream_of_or_within single fertilization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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
 
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
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

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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_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)