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Hoxd11 homeobox D11 [ Mus musculus (house mouse) ]

Gene ID: 15431, updated on 11-Apr-2024

Summary

Official Symbol
Hoxd11provided by MGI
Official Full Name
homeobox D11provided by MGI
Primary source
MGI:MGI:96203
See related
Ensembl:ENSMUSG00000042499 AllianceGenome:MGI:96203
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-4.6; Hox-5.4; Hox-5.5; E230017H14Rik
Summary
Predicted to enable DNA-binding transcription factor 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 embryonic morphogenesis; kidney development; and regionalization. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including embryo mesenchyme; genitourinary system; limb; nervous system; and skin. Orthologous to human HOXD11 (homeobox D11). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in limb E14.5 (RPKM 8.5), subcutaneous fat pad adult (RPKM 4.6) and 5 other tissues See more
Orthologs
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Genomic context

See Hoxd11 in Genome Data Viewer
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 (74509902..74517360)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (74679558..74687016)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene homeobox D13 Neighboring gene homeobox D12 Neighboring gene homeobox D10 Neighboring gene STARR-seq mESC enhancer starr_04854 Neighboring gene homeobox D9 Neighboring gene predicted gene, 38462 Neighboring gene homeobox D8

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (2) 

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
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 sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in anatomical structure development 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 branching involved in ureteric bud morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of cell development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of chondrocyte development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of chondrocyte differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within developmental growth IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within dorsal/ventral pattern formation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within embryonic digit morphogenesis IGI
Inferred from Genetic Interaction
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 limb morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within embryonic skeletal joint morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within metanephros development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within organ induction IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within pattern specification process IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within positive regulation of chondrocyte development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within positive regulation of chondrocyte differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within proximal/distal pattern formation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of chondrocyte differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
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 system development IGI
Inferred from Genetic Interaction
more info
PubMed 
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
 
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

Preferred Names
homeobox protein Hox-D11
Names
homeo box D11
homeobox protein Hox-4.6
homeobox protein Hox-5.5

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_008273.2NP_032299.1  homeobox protein Hox-D11

    See identical proteins and their annotated locations for NP_032299.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
    Source sequence(s)
    AK054090, AL928644, BC138115
    Consensus CDS
    CCDS16140.1
    UniProtKB/Swiss-Prot
    P23813
    UniProtKB/TrEMBL
    A2ASM7
    Related
    ENSMUSP00000122582.2, ENSMUST00000142312.3
    Conserved Domains (2) summary
    pfam00046
    Location:267320
    Homeobox; Homeobox domain
    pfam12045
    Location:26187
    DUF3528; Protein of unknown function (DUF3528)

RNA

  1. NR_073086.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AK054090, AL928644
    Related
    ENSMUST00000048086.9

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
    74509902..74517360
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)