Hoxd9 homeobox D9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxd9provided by MGI
Official Full Name: homeobox D9provided by MGI
Primary source: MGI:MGI:96210
See related: Ensembl:ENSMUSG00000043342 AllianceGenome:MGI:96210
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-4.4; Hox-5.2
Summary: Enables DNA binding activity and DNA-binding transcription factor activity. Acts upstream of or within several processes, including animal organ development; limb morphogenesis; and regionalization. Located in nucleus. Is expressed in several structures, including embryo mesenchyme; genitourinary system; gut; integumental system; and limb. Orthologous to human HOXD9 (homeobox D9). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in ovary adult (RPKM 21.3), subcutaneous fat pad adult (RPKM 8.5) and 7 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:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (74528107..74530552)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (74697763..74700208)

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?

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.
Gli3 mutant limbs are characterized by a severe polydactyly and associated ectopic anterior expression of 5'Hoxd genes.
Title: Hoxd and Gli3 interactions modulate digit number in the amniote limb.

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)

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

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

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:143398

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:143399

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:143400

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:536674

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:474753

D2Mit35 (e-PCR), detects polymorphism
- UniSTS:129242

D2Mit36 (e-PCR), detects polymorphism
- UniSTS:129254

D2Mit38 (e-PCR), detects polymorphism
- UniSTS:129277

D2Tfv10 (e-PCR), detects polymorphism
- UniSTS:142334

D2Mit38.1 (e-PCR), detects polymorphism
- UniSTS:129278

D2Tfv11 (e-PCR), detects polymorphism
- UniSTS:142335

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor 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	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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	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
acts_upstream_of_or_within adult locomotory behavior	IGI Inferred from Genetic Interaction more info	PubMed
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 embryonic forelimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic forelimb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IMP Inferred from Mutant Phenotype 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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within forelimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hindlimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mammary gland development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within peripheral nervous system neuron development	IGI Inferred from Genetic Interaction 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 proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within proximal/distal pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within proximal/distal pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within single fertilization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within skeletal muscle tissue development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	ISO Inferred from Sequence Orthology more info
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

General protein information

Go to the top of the page Help

Preferred Names: homeobox protein Hox-D9

Names: homeo box D9; homeobox protein Hox-4.4; homeobox protein Hox-5.2

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.