HOXD4 homeobox D4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXD4provided by HGNC
Official Full Name: homeobox D4provided by HGNC
Primary source: HGNC:HGNC:5138
See related: Ensembl:ENSG00000170166 MIM:142981; AllianceGenome:HGNC:5138
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; HOX4B; HHO.C13; HOX-5.1; Hox-4.2
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 protein encoded by this gene may play a role in determining positional values in developing limb buds. Alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
Expression: Biased expression in endometrium (RPKM 14.5), kidney (RPKM 10.9) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q31.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (176151550..176153226)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (176637994..176641368)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (177016278..177017954)

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: 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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
identified heterozygous HOXD4 loss-of-function mutations in three subjects with spinal extradural arachnoid cyst (SEDAC)
Title: Identification of HOXD4 Mutations in Spinal Extradural Arachnoid Cyst.
The results suggest that genetic polymorphisms in HOXD4 may not be a major contributor to the observed variability in peak BMD in the lumbar spine and the hip in Chinese men and women
Title: Polymorphisms in the HOXD4 gene are not associated with peak bone mineral density in Chinese nuclear families.
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.
microRNA-10a (miR-10a) targets a homologous DNA region in the promoter region of the hoxd4 gene and represses its expression at the transcriptional level
Title: Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in the HOXD4 gene are not associated with peak bone mineral density in Chinese nuclear families.

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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

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

UniSTS:480790 (e-PCR)
- UniSTS:480790

STS-X17360 (e-PCR)
- UniSTS:77133

NoName (e-PCR)
- UniSTS:482013

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
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
involved_in embryonic organ development	IEP Inferred from Expression Pattern more info	PubMed
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
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within stem cell differentiation	IEA Inferred from Electronic Annotation more info

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

General protein information

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Preferred Names: homeobox protein Hox-D4

Names: Hox-4.2, mouse, homolog of homeo box X; homeobox protein HHO.C13; homeobox protein Hox-4B; homeobox protein Hox-5.1

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.