HOXD1 homeobox D1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXD1provided by HGNC
Official Full Name: homeobox D1provided by HGNC
Primary source: HGNC:HGNC:5132
See related: Ensembl:ENSG00000128645 MIM:142987; AllianceGenome:HGNC:5132
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; HOX4G; Hox-4.7
Summary: This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. [provided by RefSeq, Jul 2008]
Expression: Broad expression in kidney (RPKM 1.7), lung (RPKM 1.6) and 16 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q31.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (176188668..176190907)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (176676799..176679038)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (177053396..177055635)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Homeobox-D 1 and FTO form a transcriptional-epigenetic feedback loop to promote head and neck cancer proliferation.
Title: Homeobox-D 1 and FTO form a transcriptional-epigenetic feedback loop to promote head and neck cancer proliferation.
A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and validation in renal cell carcinoma.
Title: A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and validation in renal cell carcinoma.
HOXD1 functions as a novel tumor suppressor in kidney renal clear cell carcinoma.
Title: HOXD1 functions as a novel tumor suppressor in kidney renal clear cell carcinoma.
Data indicate that median methylation levels of BCAN, HOXD1, KCTD8, KLF11, NXPH1, POU4F1, SIM1, and TCF7L1 were >/=30% higher than in normal samples, representing potential biomarkers for tumor diagnosis.
Title: Genome-wide methylation screen in low-grade breast cancer identifies novel epigenetically altered genes as potential biomarkers for tumor diagnosis.
HOXD1 plays a significant role in endothelial cells functions by regulating the expression of ITGB1.
Title: Homeobox D1 regulates angiogenic functions of endothelial cells via integrin β1 expression.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
Single nucleotide polymorphism in HOXD1 is associated with ovarian cancer.
Title: A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.

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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

EBI GWAS Catalog

Description
A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. EBI GWAS Catalog EBI GWAS 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

HOXD1_1231 (e-PCR)
- UniSTS:277323

RH68884 (e-PCR)
- UniSTS:111

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	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
involved_in sensory perception of pain	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein Hox-D1

Names: homeo box 4G; homeo box D1; homeobox protein Hox-GG

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.