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    Whrn whirlin [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313255, updated on 9-Sep-2018

    Summary

    Official Symbol
    Whrnprovided by RGD
    Official Full Name
    whirlinprovided by RGD
    Primary source
    RGD:631330
    See related
    Ensembl:ENSRNOG00000001700
    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
    Also known as
    Cip98; Dfnb31
    Summary
    interacts with calmodulin-dependent serine kinase Cask; may play a a role in synaptic transmission [RGD, Feb 2006]
    Annotation information
    Annotation category: partial on reference assembly
    Expression
    Biased expression in Adrenal (RPKM 50.6), Thymus (RPKM 50.4) and 8 other tissues See more
    Orthologs

    Genomic context

    See Whrn in Genome Data Viewer
    Location:
    5q24
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (79235541..79317206, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 5 NC_005104.3 (83349720..83431410, complement)

    Chromosome 5 - NC_005104.4Genomic Context describing neighboring genes Neighboring gene orosomucoid 1 Neighboring gene AT-hook transcription factor Neighboring gene uncharacterized LOC102547858 Neighboring gene H/ACA ribonucleoprotein complex subunit 3 pseudogene Neighboring gene ATPase H+ transporting V1 subunit G1

    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

    Bibliography

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    auditory receptor cell stereocilium organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    auditory receptor cell stereocilium organization IEA
    Inferred from Electronic Annotation
    more info
     
    auditory receptor cell stereocilium organization ISO
    Inferred from Sequence Orthology
    more info
     
    cerebellar Purkinje cell layer formation IEA
    Inferred from Electronic Annotation
    more info
     
    cerebellar Purkinje cell layer formation ISO
    Inferred from Sequence Orthology
    more info
     
    establishment of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    establishment of protein localization ISO
    Inferred from Sequence Orthology
    more info
     
    inner ear receptor cell stereocilium organization ISO
    Inferred from Sequence Orthology
    more info
     
    inner ear receptor cell stereocilium organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    paranodal junction maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    paranodal junction maintenance ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    retina homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    retina homeostasis ISO
    Inferred from Sequence Orthology
    more info
     
    sensory perception of light stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    sensory perception of light stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    USH2 complex IEA
    Inferred from Electronic Annotation
    more info
     
    USH2 complex ISO
    Inferred from Sequence Orthology
    more info
     
    actin filament IEA
    Inferred from Electronic Annotation
    more info
     
    actin filament ISO
    Inferred from Sequence Orthology
    more info
     
    axon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ciliary basal body IEA
    Inferred from Electronic Annotation
    more info
     
    ciliary basal body ISO
    Inferred from Sequence Orthology
    more info
     
    cilium ISO
    Inferred from Sequence Orthology
    more info
     
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    dendrite IDA
    Inferred from Direct Assay
    more info
    PubMed 
    dendritic shaft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    growth cone IEA
    Inferred from Electronic Annotation
    more info
     
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuronal cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with neuronal cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    periciliary membrane compartment IEA
    Inferred from Electronic Annotation
    more info
     
    periciliary membrane compartment ISO
    Inferred from Sequence Orthology
    more info
     
    colocalizes_with photoreceptor connecting cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    colocalizes_with photoreceptor connecting cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    photoreceptor connecting cilium IEA
    Inferred from Electronic Annotation
    more info
     
    photoreceptor connecting cilium ISO
    Inferred from Sequence Orthology
    more info
     
    colocalizes_with photoreceptor inner segment IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    colocalizes_with photoreceptor inner segment IDA
    Inferred from Direct Assay
    more info
    PubMed 
    photoreceptor inner segment IEA
    Inferred from Electronic Annotation
    more info
     
    photoreceptor inner segment ISO
    Inferred from Sequence Orthology
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    stereocilia ankle link IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    stereocilia ankle link ISO
    Inferred from Sequence Orthology
    more info
     
    stereocilia ankle link complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    stereocilia ankle link complex IEA
    Inferred from Electronic Annotation
    more info
     
    stereocilia ankle link complex ISO
    Inferred from Sequence Orthology
    more info
     
    stereocilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    stereocilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    stereocilium ISO
    Inferred from Sequence Orthology
    more info
     
    stereocilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    stereocilium bundle ISO
    Inferred from Sequence Orthology
    more info
     
    stereocilium tip IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    stereocilium tip IEA
    Inferred from Electronic Annotation
    more info
     
    stereocilium tip ISO
    Inferred from Sequence Orthology
    more info
     
    synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    whirlin
    Names
    CASK-interacting protein CIP98
    deafness, autosomal recessive 31

    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_181088.1NP_851602.1  whirlin

      See identical proteins and their annotated locations for NP_851602.1

      Status: PROVISIONAL

      Source sequence(s)
      AY227205
      UniProtKB/Swiss-Prot
      Q810W9
      Related
      ENSRNOP00000002309.2, ENSRNOT00000002309.2
      Conserved Domains (3) summary
      cd00992
      Location:139216
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd07356
      Location:38113
      HN_L-whirlin_R1_like; first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains
      cd07357
      Location:418498
      HN_L-whirlin_R2_like; second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains

    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_005104.4 Reference Rnor_6.0 Primary Assembly

      Range
      79235541..79317206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate Rn_Celera

    Genomic

    1. AC_000073.1 Alternate Rn_Celera

      Range
      75762917..75845137 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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