HOXD9 homeobox D9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXD9provided by HGNC
Official Full Name: homeobox D9provided by HGNC
Primary source: HGNC:HGNC:5140
See related: Ensembl:ENSG00000128709 MIM:142982
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: mouse all

Genomic context

Location:: 2q31.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
109.20200522	current	GRCh38.p13 (GCF_000001405.39)	2	NC_000002.12 (176122719..176124937)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (176987413..176989645)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

High expression of HOXD9 was correlated with poor survival in gastric cancer.
Title: HOXD9 promotes the growth, invasion and metastasis of gastric cancer cells by transcriptional activation of RUFY3.
HOXD9 promotes epithelial-mesenchymal transition and cancer metastasis by ZEB1 regulation in hepatocellular carcinoma
Title: HOXD9 promotes epithelial-mesenchymal transition and cancer metastasis by ZEB1 regulation in hepatocellular carcinoma.
HoxD9 expression is regulated by histone acetylation in endothelial progenitor cells
Title: Histone acetylation regulates the expression of HoxD9 transcription factor in endothelial progenitor cells.
Data show that overexpressing homeobox D9 protein HOXD9 in mucinous ovarian carcinomas (MOCs)cells augmented the neoplastic phenotype
Title: Genome-wide significant risk associations for mucinous ovarian carcinoma.
The study investigates the temperature dependence of the internal motions of the lysine side-chain NH3(+) groups that form ion pairs with DNA phosphate groups in the HoxD9 homeodomain-DNA complex.
Title: Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds.
Results show that melanoma patients with HOXD9 hypermethylation in lymph node metastasis had poorer disease-free and overall survival.
Title: Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis.
A genome-wide array-comparative genomic hybridization (aCGH) analysis revealed global chromosomal aberration in MWCNTs-treated clones, predominantly at chromosome 2q31-32, where the potential oncogenes HOXD9 and HOXD13 are located
Title: Focal amplification of HOXD-harboring chromosome region is implicated in multiple-walled carbon nanotubes-induced carcinogenicity.
The association between SNP of the HOXD9 gene and developmental hip dysplasia reached significance in Chinese Han females.
Title: Association analysis between HOXD9 genes and the development of developmental dysplasia of the hip in Chinese female Han population.
Our results suggest that HOXD9 may be a novel marker of GCSCs and cell proliferation and/or survival factor in gliomas and glioma cancer stem-like cells, and a potential therapeutic target.
Title: Functional analysis of HOXD9 in human gliomas and glioma cancer stem cells.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

NHGRI GWAS Catalog

Description
Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:143399

HOXD9_1230 (e-PCR)
- UniSTS:277324

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:474753

RH18119 (e-PCR)
- UniSTS:49395

Homology

Homologs of the HOXD9 gene: The HOXD9 gene is conserved in chimpanzee, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 290 organisms have orthologs with human gene HOXD9
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
RNA polymerase II proximal promoter sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
RNA polymerase II regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
adult locomotory behavior	IEA Inferred from Electronic Annotation more info
anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info	PubMed
embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
mammary gland development	IEA Inferred from Electronic Annotation more info
negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
peripheral nervous system neuron development	IEA Inferred from Electronic Annotation more info
positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
single fertilization	IEA Inferred from Electronic Annotation more info
skeletal muscle tissue development	IEA Inferred from Electronic Annotation more info
transcription, DNA-templated	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
nuclear chromatin	ISA Inferred from Sequence Alignment more info
nucleolus	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

General protein information

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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

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.