Hoxd13 homeobox D13 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxd13provided by MGI
Official Full Name: homeobox D13provided by MGI
Primary source: MGI:MGI:96205
See related: Ensembl:ENSMUSG00000001819 AllianceGenome:MGI:96205
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: spdh; Hox-4.8
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Acts upstream of or within several processes, including embryonic digit morphogenesis; morphogenesis of an epithelium; and regulation of branching involved in prostate gland morphogenesis. Located in nucleus. Is expressed in several structures, including genitourinary system; hindgut; limb; limb bud; and tail. Used to study synpolydactyly. Human ortholog(s) of this gene implicated in brachydactyly-syndactyly syndrome; clubfoot; cryptorchidism; and dysostosis (multiple). Orthologous to human HOXD13 (homeobox D13). [provided by Alliance of Genome Resources, Jul 2025]
Expression: Biased expression in limb E14.5 (RPKM 44.7), colon adult (RPKM 15.1) and 1 other tissue See more
Orthologs: all
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Genomic context

Location:: 2 C3; 2 44.13 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (74498569..74501947)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (74668225..74671603)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel Hoxd13 mutation causes synpolydactyly and promotes osteoclast differentiation by regulating pSmad5/p65/c-Fos/Rank axis.
Title: A novel Hoxd13 mutation causes synpolydactyly and promotes osteoclast differentiation by regulating pSmad5/p65/c-Fos/Rank axis.
Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations.
Title: Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations.
Geminin is required for Hox gene regulation to pattern the developing limb.
Title: Geminin is required for Hox gene regulation to pattern the developing limb.
TLR2/6 signaling promotes the expansion of premalignant hematopoietic stem and progenitor cells in the NUP98-HOXD13 mouse model of MDS.
Title: TLR2/6 signaling promotes the expansion of premalignant hematopoietic stem and progenitor cells in the NUP98-HOXD13 mouse model of MDS.
NHD13 transgenic mice lacking Lyl1 showed accelerated T-ALL and absence of transformation to AML, associated with a loss of multipotent progenitors in the bone marrow.
Title: The NUP98-HOXD13 fusion oncogene induces thymocyte self-renewal via Lmo2/Lyl1.
we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13(-/-); Hoxd13(-/-) limbs.
Title: Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13.
The age-associated accumulation of somatic mutations that occurs in the Nup98-HOXD13 (NHD13) mouse model of leukemia progression was significantly elevated by co-expression of a PKR transgene.
Title: PKR inhibits the DNA damage response, and is associated with poor survival in AML and accelerated leukemia in NHD13 mice.
Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13.
Title: Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb.
Data indicate that loss of cyclin-dependent kinase inhibitor p15 (p15Ink4b) collaborates with oncogene fusion protein Nup98-HoxD13 transgene in the development of predominantly myeloid neoplasms.
Title: Brief report: Loss of p15Ink4b accelerates development of myeloid neoplasms in Nup98-HoxD13 transgenic mice.
study elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype; results show that the mutation results in a shift in the binding profile of the mutant toward a bicoid/PITX1 motif
Title: Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (8) 1 citation
Spontaneous (2) 1 citation
Targeted (8) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:484895

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:143395

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:225863

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:536670

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:265598

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:547820

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	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	IEA Inferred from Electronic Annotation 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 cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within branch elongation of an epithelium	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic digit morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in embryonic hindgut morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic hindgut morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gland morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within limb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within male genitalia development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within morphogenesis of an epithelial fold	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pattern specification process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pattern specification process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in prostate gland development	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 branching involved in prostate gland morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to testosterone	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-D13

Names: homeo box D13; homeobox protein Hox-4.8

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.