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    Hoxd9 homeo box D9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 688999, updated on 4-Jan-2025

    Summary

    Official Symbol
    Hoxd9provided by RGD
    Official Full Name
    homeo box D9provided by RGD
    Primary source
    RGD:1582908
    See related
    EnsemblRapid:ENSRNOG00000001580 AllianceGenome:RGD:1582908
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in embryonic skeletal system morphogenesis; negative regulation of transcription by RNA polymerase II; and regionalization. Predicted to act upstream of or within several processes, including embryonic skeletal system development; limb morphogenesis; and peripheral nervous system neuron development. Predicted to be located in nucleolus and nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXD9 (homeobox D9). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Biased expression in Kidney (RPKM 75.3), Uterus (RPKM 36.4) and 3 other tissues See more
    Orthologs
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    Genomic context

    See Hoxd9 in Genome Data Viewer
    Location:
    3q23
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (80008006..80010186)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (59600575..59602755)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (61620192..61622360)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene homeobox D11 Neighboring gene homeo box D10 Neighboring gene homeobox D8 Neighboring gene uncharacterized LOC120101573 Neighboring gene homeo box D4

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Pathways from PubChem

    General gene information

    Clone Names

    • MGC189507

    Gene Ontology Provided by RGD

    Items 1 - 25 of 32
    Process Evidence Code Pubs
    involved_in DNA-templated transcription  
    involved_in adult locomotory behavior  
    acts_upstream_of_or_within adult locomotory behavior  
    involved_in anterior/posterior pattern specification  
    involved_in anterior/posterior pattern specification  
    acts_upstream_of_or_within anterior/posterior pattern specification  
    involved_in embryonic forelimb morphogenesis  
    acts_upstream_of_or_within embryonic forelimb morphogenesis  
    acts_upstream_of_or_within embryonic skeletal system development  
    involved_in embryonic skeletal system morphogenesis  
    involved_in embryonic skeletal system morphogenesis  
    acts_upstream_of_or_within embryonic skeletal system morphogenesis  
    acts_upstream_of_or_within forelimb morphogenesis  
    involved_in hindlimb morphogenesis  
    acts_upstream_of_or_within hindlimb morphogenesis  
    involved_in mammary gland development  
    acts_upstream_of_or_within mammary gland development  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in negative regulation of transcription by RNA polymerase II  
    involved_in peripheral nervous system neuron development  
    acts_upstream_of_or_within peripheral nervous system neuron development  
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in proximal/distal pattern formation  
    involved_in proximal/distal pattern formation  
    acts_upstream_of_or_within proximal/distal pattern formation  
    acts_upstream_of_or_within regulation of gene expression  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in single fertilization  
    acts_upstream_of_or_within single fertilization  
    involved_in skeletal muscle tissue development  
    acts_upstream_of_or_within skeletal muscle tissue development  
    Items 1 - 25 of 32
    Component Evidence Code Pubs
    located_in nucleolus  
    located_in nucleolus  
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus  

    General protein information

    Preferred Names
    homeobox protein Hox-D9
    Names
    homeobox Hox-D9

    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_001173469.2NP_001166940.1  homeobox protein Hox-D9

      See identical proteins and their annotated locations for NP_001166940.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/Swiss-Prot
      B5DFK3
      UniProtKB/TrEMBL
      D4A2V8
      Related
      ENSRNOP00000059218.4, ENSRNOT00000065426.5
      Conserved Domains (2) summary
      smart00389
      Location:276328
      HOX; Homeodomain
      pfam04617
      Location:1155
      Hox9_act; Hox9 activation region

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      80008006..80010186
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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