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    Pcdh15 protocadherin related 15 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 690865, updated on 9-Dec-2024

    Summary

    Symbol
    Pcdh15provided by RGD
    Full Name
    protocadherin related 15provided by RGD
    Primary source
    RGD:1590969
    See related
    EnsemblRapid:ENSRNOG00000000606 AllianceGenome:RGD:1590969
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable calcium ion binding activity. Involved in response to calcium ion. Predicted to be located in several cellular components, including extracellular space; photoreceptor outer segment; and synapse. Predicted to be active in plasma membrane and stereocilium. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; Usher syndrome type 1F; and autosomal recessive nonsyndromic deafness 23. Orthologous to human PCDH15 (protocadherin related 15). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 29.9), Spleen (RPKM 11.9) and 3 other tissues See more
    Orthologs
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    Genomic context

    See Pcdh15 in Genome Data Viewer
    Location:
    20p12-p11
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (13996383..15495206, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (13997094..15496446, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (14952213..15334745, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene polymerase (RNA) III (DNA directed) polypeptide D, pseudogene 1 Neighboring gene uncharacterized LOC108353250 Neighboring gene uncharacterized LOC120098844 Neighboring gene uncharacterized LOC120098846 Neighboring gene uncharacterized LOC120098845 Neighboring gene transfer RNA alanine (anticodon AGC) 95 Neighboring gene uncharacterized LOC108349009 Neighboring gene transfer RNA proline (anticodon AGG) 62 Neighboring gene uncharacterized LOC134483786 Neighboring gene ZW10 interacting kinetochore protein Neighboring gene uncharacterized LOC134483787

    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

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calcium ion binding  
    enables protein binding PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within actin filament organization  
    acts_upstream_of_or_within adult locomotory behavior  
    acts_upstream_of_or_within adult walking behavior  
    acts_upstream_of_or_within auditory receptor cell stereocilium organization  
    involved_in cell adhesion  
    acts_upstream_of_or_within detection of mechanical stimulus involved in equilibrioception  
    acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound  
    involved_in equilibrioception  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules  
    acts_upstream_of_or_within inner ear auditory receptor cell differentiation  
    acts_upstream_of_or_within inner ear development  
    acts_upstream_of_or_within inner ear receptor cell stereocilium organization  
    acts_upstream_of_or_within locomotory behavior  
    acts_upstream_of_or_within morphogenesis of an epithelium  
    acts_upstream_of_or_within multicellular organism growth  
    acts_upstream_of_or_within non-motile cilium assembly  
    involved_in photoreceptor cell maintenance  
    involved_in response to calcium ion PubMed 
    acts_upstream_of_or_within righting reflex  
    involved_in sensory perception of light stimulus  
    acts_upstream_of_or_within sensory perception of sound  
    involved_in sensory perception of sound  
    acts_upstream_of_or_within startle response  
    acts_upstream_of_or_within visual perception  
    Component Evidence Code Pubs
    located_in cytoplasm  
    located_in extracellular space  
    located_in photoreceptor outer segment  
    is_active_in plasma membrane  
    located_in plasma membrane  
    is_active_in stereocilium  
    located_in stereocilium  
    located_in synapse  

    General protein information

    Preferred Names
    protocadherin-15
    Names
    protocadherin 15

    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_001271377.2NP_001258306.2  protocadherin-15 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      F1LXN4
      Related
      ENSRNOP00000060829.5, ENSRNOT00000067633.6

    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_086038.1 Reference GRCr8

      Range
      13996383..15495206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279549.1XP_063135619.1  protocadherin-15 isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y0L1
    2. XM_063279551.1XP_063135621.1  protocadherin-15 isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y0L1
    3. XM_063279550.1XP_063135620.1  protocadherin-15 isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y0L1
      Related
      ENSRNOP00000076657.2, ENSRNOT00000112877.2
    4. XM_063279552.1XP_063135622.1  protocadherin-15 isoform X2

      UniProtKB/TrEMBL
      A0A8I5Y0L1
    5. XM_063279553.1XP_063135623.1  protocadherin-15 isoform X3

      UniProtKB/TrEMBL
      F1LXN4
      Related
      ENSRNOP00000084743.2, ENSRNOT00000098841.2
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