Hoxd3 homeobox D3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxd3provided by MGI
Official Full Name: homeobox D3provided by MGI
Primary source: MGI:MGI:96207
See related: Ensembl:ENSMUSG00000079277 AllianceGenome:MGI:96207
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: Hox-4.1; Hox-5.5
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including glossopharyngeal nerve morphogenesis; skeletal system development; and thyroid gland development. Predicted to be located in aggresome and nuclear body. Predicted to be active in nucleus. Is expressed in several structures, including branchial arch; central nervous system; embryo mesenchyme; genitourinary system; and gut. Orthologous to human HOXD3 (homeobox D3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in ovary adult (RPKM 19.8), genital fat pad adult (RPKM 17.5) and 11 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2 C3; 2 44.13 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (74542337..74578615)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (74711993..74748271)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These data suggest that Hoxd3 is constitutively expressed in the skin of mid-gestational mice
Title: Homeobox genes Hoxd3 and Hoxd8 are differentially expressed in fetal mouse excisional wounds.
Results suggest that members of the Hox groups (Hoxa3, Hoxb3, Hoxd3) coordinate both suppression and activation mechanisms that ensure distinction between the multiple rhombomeres in the developing hindbrain.
Title: Hox3 genes coordinate mechanisms of genetic suppression and activation in the generation of branchial and somatic motoneurons.

Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (2) 1 citation
Targeted (3) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

AI448005 (e-PCR)
- UniSTS:158976

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

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

Hoxd3 (e-PCR), detects polymorphism
- UniSTS:143396

Hoxd4 (e-PCR), detects polymorphism
- UniSTS:143397

RH135978 (e-PCR)
- UniSTS:209974

NoName (e-PCR)
- UniSTS:491330

UniSTS:467540 (e-PCR)
- UniSTS:467540

Hoxd3 (e-PCR), detects polymorphism
- UniSTS:467540

Hoxd3 (e-PCR), detects polymorphism
- UniSTS:536671

NoName (e-PCR)
- UniSTS:234431

BB104313 (e-PCR)
- UniSTS:207345

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
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, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor 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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in Notch signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within anterior/posterior pattern specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glossopharyngeal nerve morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neuron differentiation	IGI Inferred from Genetic Interaction 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 regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within thyroid gland development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in aggresome	IEA Inferred from Electronic Annotation more info
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: homeobox protein Hox-D3

Names: homeo box D3; homeo box D4; homeobox protein Hox-4.1; homeobox protein MH-19

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.