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Hoxd9 homeobox D9 [ Mus musculus (house mouse) ]

Gene ID: 15438, updated on 8-Feb-2024

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
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Genomic context

See Hoxd9 in Genome Data Viewer
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_000068.8Genomic Context describing neighboring genes Neighboring gene homeobox D12 Neighboring gene homeobox D11 Neighboring gene STARR-seq mESC enhancer starr_04854 Neighboring gene homeobox D10 Neighboring gene predicted gene, 38462 Neighboring gene homeobox D8 Neighboring gene homeobox D3, opposite strand 1 Neighboring gene homeobox D3

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (1) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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

Preferred Names
homeobox protein Hox-D9
Names
homeo box D9
homeobox protein Hox-4.4
homeobox protein Hox-5.2

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)

  1. NM_013555.4NP_038583.1  homeobox protein Hox-D9

    See identical proteins and their annotated locations for NP_038583.1

    Status: VALIDATED

    Source sequence(s)
    AK134427, AL928644
    Consensus CDS
    CCDS16142.1
    UniProtKB/Swiss-Prot
    A2ASM9, P28357, Q3UMQ3, Q3UYS2
    Related
    ENSMUSP00000058490.9, ENSMUST00000059272.10
    Conserved Domains (2) summary
    smart00389
    Location:272324
    HOX; Homeodomain
    pfam04617
    Location:1153
    Hox9_act; Hox9 activation region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    74528107..74530552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)