HOXD3 homeobox D3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXD3provided by HGNC
Official Full Name: homeobox D3provided by HGNC
Primary source: HGNC:HGNC:5137
See related: Ensembl:ENSG00000128652 MIM:142980; AllianceGenome:HGNC:5137
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: mouse all
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Genomic context

Location:: 2q31.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (176152529..176173098)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (176640671..176661238)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (177022035..177037826)

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.
Identification and validation of HOXD3 and UNC5C as molecular signatures in keloid based on weighted gene co-expression network analysis.
Title: Identification and validation of HOXD3 and UNC5C as molecular signatures in keloid based on weighted gene co-expression network analysis.
HOXD3 Up-regulating KDM5C Promotes Malignant Progression of Diffuse Large B-Cell Lymphoma by Decreasing p53 Expression
Title: HOXD3 Up-regulating KDM5C Promotes Malignant Progression of Diffuse Large B-Cell Lymphoma by Decreasing p53 Expression.
HOXD3 was negatively regulated by YY1 recruiting HDAC1 to suppress progression of hepatocellular carcinoma cells via ITGA2 pathway.
Title: HOXD3 was negatively regulated by YY1 recruiting HDAC1 to suppress progression of hepatocellular carcinoma cells via ITGA2 pathway.
Nuclear lncRNA HOXD-AS1 suppresses colorectal carcinoma growth and metastasis via inhibiting HOXD3-induced ITGB3 transcriptional activation and MAPK/AKT signaling.
Title: Nuclear lncRNA HOXD-AS1 suppresses colorectal carcinoma growth and metastasis via inhibiting HOXD3-induced integrin β3 transcriptional activating and MAPK/AKT signalling.
The findings indicate that miR-203a inhibits hepatocellular carcinoma cell invasion, metastasis, and angiogenesis by negatively targeting HOXD3 and suppressing cell signaling through the VEGFR pathway.
Title: HOXD3 targeted by miR-203a suppresses cell metastasis and angiogenesis through VEGFR in human hepatocellular carcinoma cells.
EGR1 is a key player in the transcriptional control of miR-203a, and that miR-203a acts as an anti-oncogene to suppress HCC tumorigenesis by targeting HOXD3 through EGFR-related cell signaling pathways.
Title: EGR1 mediates miR-203a suppress the hepatocellular carcinoma cells progression by targeting HOXD3 through EGFR signaling pathway.
the HOXD3 gene promotes colorectal cancer cell growth and plays a pivotal role in the development and survival of malignant human colorectal cancer cells.
Title: RNAi-mediated HOXD3 knockdown inhibits growth in human RKO cells.
These results validate the association between promoter hypermethylation of ABHD9 and HOXD3 and prostate cancer recurrence
Title: Validation study of genes with hypermethylated promoter regions associated with prostate cancer recurrence.
describe familial cases of TH in two generations (proband and his father), in addition to other two sporadic cases. We have found polymorphisms in the HOXB3, HOXD3, and a new synonymous variant, and PITX2 genes
Title: The absence of mutations in homeobox candidate genes HOXA3, HOXB3, HOXD3 and PITX2 in familial and sporadic thyroid hemiagenesis.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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

Hoxd3 (e-PCR), detects polymorphism
- UniSTS:158733

RH69263 (e-PCR)
- UniSTS:74134

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
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 RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay 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 DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterior/posterior pattern specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in cartilage development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-matrix adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryonic skeletal system morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in glossopharyngeal nerve morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in thyroid gland development	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in aggresome	IDA Inferred from Direct Assay more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in nuclear body	IDA Inferred from Direct Assay 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
located_in nucleus	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: homeobox protein Hox-D3

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

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.

mRNA and Protein(s)

NM_006898.5 → NP_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, Q99955, Q9BSC5

Related

ENSP00000507129.1, ENST00000683222.1

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

176152529..176173098

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047444092.1 → XP_047300048.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_047444087.1 → XP_047300043.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_047444090.1 → XP_047300046.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_011511066.4 → XP_011509368.1 homeobox protein Hox-D3 isoform X1

See identical proteins and their annotated locations for XP_011509368.1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)
XM_005246511.5 → XP_005246568.1 homeobox protein Hox-D3 isoform X1

See identical proteins and their annotated locations for XP_005246568.1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)
XM_005246509.5 → XP_005246566.1 homeobox protein Hox-D3 isoform X1

See identical proteins and their annotated locations for XP_005246566.1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5

Related

ENSP00000386498.1, ENST00000410016.5

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)
XM_011511065.4 → XP_011509367.1 homeobox protein Hox-D3 isoform X1

See identical proteins and their annotated locations for XP_011509367.1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)
XM_047444089.1 → XP_047300045.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_047444088.1 → XP_047300044.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

176640671..176661238

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054341658.1 → XP_054197633.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341651.1 → XP_054197626.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341656.1 → XP_054197631.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341657.1 → XP_054197632.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341653.1 → XP_054197628.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341655.1 → XP_054197630.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341654.1 → XP_054197629.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5
XM_054341652.1 → XP_054197627.1 homeobox protein Hox-D3 isoform X1

UniProtKB/Swiss-Prot

P31249, Q99955, Q9BSC5