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    Hoxd11 homeobox D11 [ Mus musculus (house mouse) ]

    Gene ID: 15431, updated on 18-Sep-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
    NEW
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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 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)
    • Endonuclease-mediated (2) 
    • Targeted (6)  1 citation

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    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 
    involved_in embryonic skeletal joint morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 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 
    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
     
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    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)

    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.

    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)