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    Cdh23 cadherin-related 23 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 114102, updated on 2-Nov-2024

    Summary

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    Symbol
    Cdh23provided by RGD
    Full Name
    cadherin-related 23provided by RGD
    Primary source
    RGD:619760
    See related
    EnsemblRapid:ENSRNOG00000033087 AllianceGenome:RGD:619760
    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. Predicted to be involved in several processes, including equilibrioception; photoreceptor cell maintenance; and regulation of cytosolic calcium ion concentration. Predicted to act upstream of or within several processes, including inner ear development; righting reflex; and sensory perception of sound. Located in apical part of cell. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; autosomal recessive nonsyndromic deafness; autosomal recessive nonsyndromic deafness 12; and pituitary adenoma 5. Orthologous to human CDH23 (cadherin related 23). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 29.8), Testes (RPKM 29.4) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cdh23 in Genome Data Viewer
    Location:
    20q11
    Exon count:
    74
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (28783124..29165624, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (28240643..28622490, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (29857018..30263758, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene carbohydrate sulfotransferase 3 Neighboring gene ribosomal protein L37A, pseudogene 15 Neighboring gene prosaposin Neighboring gene uncharacterized LOC134483915 Neighboring gene similar to human chromosome 10 open reading frame 105 Neighboring gene V-set immunoregulatory receptor Neighboring gene solute carrier family 29 member 3 Neighboring gene unc-5 netrin receptor B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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    Related articles in PubMed

    1. Cadherin 23 is a component of the transient lateral links in the developing hair bundles of cochlear sensory cells. Michel V, et al. Dev Biol, 2005 Apr 15. PMID 15882573
    2. Vestibulocochlear defects and effects of deuterium oxide in mutant bustling (BUS) mice. Otani H, et al. Acta Otolaryngol Suppl, 1995. PMID 7610888
    3. Degenerative hairlets on the vestibular sensory cells in mutant bustling (BUS/Idr) mice. Moriyama K, et al. Acta Otolaryngol, 1997 Jan. PMID 9039475
    4. Association of cadherin 23 with polygenic inheritance and genetic modification of sensorineural hearing loss. Noben-Trauth K, et al. Nat Genet, 2003 Sep. PMID 12910270, Free PMC Article
    5. Age-related hearing loss and the ahl locus in mice. Keithley EM, et al. Hear Res, 2004 Feb. PMID 14759567, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data indicate that CNGA3 interacts with cadherin 23 and with cadherin 23 binding partner, myosin VIIa.
      Title: Cyclic nucleotide-gated channel α-3 (CNGA3) interacts with stereocilia tip-link cadherin 23 + exon 68 or alternatively with myosin VIIa, two proteins required for hair cell mechanotransduction.
    2. Cadherin 23 is a component of the transient lateral links in the developing hair bundles of cochlear sensory cells
      Title: Cadherin 23 is a component of the transient lateral links in the developing hair bundles of cochlear sensory cells.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in auditory receptor cell stereocilium organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within auditory receptor cell stereocilium organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in calcium ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in calcium ion transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cochlea development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cochlea development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in equilibrioception IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in equilibrioception ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within inner ear auditory receptor cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within inner ear development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within inner ear morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within inner ear receptor cell stereocilium organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in photoreceptor cell maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in photoreceptor cell maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cytosolic calcium ion concentration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cytosolic calcium ion concentration ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within righting reflex ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of light stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within sensory perception of light stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of light stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cochlear hair cell ribbon synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cochlear hair cell ribbon synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in kinocilium IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in kinocilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor inner segment IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in photoreceptor inner segment ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor ribbon synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in photoreceptor ribbon synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in stereocilium tip IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium tip ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-23
    Names
    Waltzing
    cadherin 23 (otocadherin)
    cadherin-23-like
    otocadherin

    NCBI Reference Sequences (RefSeq)

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    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_053644.2 → NP_446096.2  cadherin-23 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/Swiss-Prot
      P58365
      Related
      ENSRNOP00000096099.1, ENSRNOT00000118579.2
      Conserved Domains (1) summary
      cd11304
      Location:1531 → 1628
      Cadherin_repeat; Cadherin tandem repeat domain

    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
      28783124..29165624 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063278917.1 → XP_063134987.1  cadherin-23 isoform X3

    2. XM_063278916.1 → XP_063134986.1  cadherin-23 isoform X2

    3. XM_063278914.1 → XP_063134984.1  cadherin-23 isoform X1

    4. XM_063278918.1 → XP_063134988.1  cadherin-23 isoform X4

    5. XM_063278915.1 → XP_063134985.1  cadherin-23 isoform X1

    6. XM_063278919.1 → XP_063134989.1  cadherin-23 isoform X5

    7. XM_063278920.1 → XP_063134990.1  cadherin-23 isoform X6

    8. XM_063278921.1 → XP_063134991.1  cadherin-23 isoform X7

    9. XM_063278923.1 → XP_063134993.1  cadherin-23 isoform X9

    10. XM_063278922.1 → XP_063134992.1  cadherin-23 isoform X8

    11. XM_063278926.1 → XP_063134996.1  cadherin-23 isoform X11

    12. XM_063278925.1 → XP_063134995.1  cadherin-23 isoform X10

    13. XM_063278927.1 → XP_063134997.1  cadherin-23 isoform X12

    14. XM_063278928.1 → XP_063134998.1  cadherin-23 isoform X13

    15. XM_039098377.2 → XP_038954305.1  cadherin-23 isoform X14

      Conserved Domains (1) summary
      cd11304
      Location:892 → 988
      Cadherin_repeat; Cadherin tandem repeat domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P58365.1 GenPept UniProtKB/Swiss-Prot:P58365

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials