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    Capn6 calpain 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 83685, updated on 21-Jul-2018

    Summary

    Official Symbol
    Capn6provided by RGD
    Official Full Name
    calpain 6provided by RGD
    Primary source
    RGD:70960
    See related
    Ensembl:ENSRNOG00000004882
    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
    human and mouse homologs lack the calmodulin-like domain present in other members of the calpain family of calcium-dependent, cysteine proteases and may be proteolytically inactive [RGD, Feb 2006]
    Expression
    Biased expression in Muscle (RPKM 71.2), Kidney (RPKM 24.2) and 6 other tissues See more
    Orthologs

    Genomic context

    See Capn6 in Genome Data Viewer
    Location:
    Xq33
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (115049113..115073824, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) X NC_005120.3 (113502312..113527023, complement)

    Chromosome X - NC_005120.4Genomic Context describing neighboring genes Neighboring gene chordin-like 1 Neighboring gene p21 (RAC1) activated kinase 3 Neighboring gene doublecortin Neighboring gene similar to cell division cycle 2-like 1

    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 BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    calcium-dependent cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium-dependent cysteine-type endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
     
    microtubule binding IEA
    Inferred from Electronic Annotation
    more info
     
    microtubule binding ISO
    Inferred from Sequence Orthology
    more info
     
    microtubule binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    microtubule bundle formation IEA
    Inferred from Electronic Annotation
    more info
     
    microtubule bundle formation ISO
    Inferred from Sequence Orthology
    more info
     
    microtubule bundle formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    proteolysis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    proteolysis IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
     
    regulation of cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    microtubule IEA
    Inferred from Electronic Annotation
    more info
     
    microtubule ISO
    Inferred from Sequence Orthology
    more info
     
    perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    spindle IEA
    Inferred from Electronic Annotation
    more info
     
    spindle microtubule IEA
    Inferred from Electronic Annotation
    more info
     
    spindle microtubule ISO
    Inferred from Sequence Orthology
    more info
     

    NCBI Reference Sequences (RefSeq)

    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_031808.1NP_113996.1  calpain-6

      See identical proteins and their annotated locations for NP_113996.1

      Status: PROVISIONAL

      Source sequence(s)
      AF067793
      UniProtKB/Swiss-Prot
      O88501
      Related
      ENSRNOP00000006638.1, ENSRNOT00000006638.3
      Conserved Domains (3) summary
      smart00230
      Location:13351
      CysPc; Calpain-like thiol protease family
      cd04046
      Location:514639
      C2_Calpain; C2 domain present in Calpain proteins
      cd00214
      Location:349497
      Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005120.4 Reference Rnor_6.0 Primary Assembly

      Range
      115049113..115073824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000089.1 Alternate Rn_Celera

      Range
      106779922..106804635 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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