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    Ccdc50 coiled-coil domain containing 50 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 288022, updated on 25-Apr-2024

    Summary

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    Official Symbol
    Ccdc50provided by RGD
    Official Full Name
    coiled-coil domain containing 50provided by RGD
    Primary source
    RGD:727841
    See related
    Ensembl:ENSRNOG00000001930 AllianceGenome:RGD:727841
    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
    Also known as
    c3orf6; C3orf6h
    Summary
    Predicted to enable ubiquitin protein ligase binding activity. Predicted to act upstream of or within sensory perception of sound. Predicted to be located in cytosol and microtubule cytoskeleton. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 44 and mantle cell lymphoma. Orthologous to human CCDC50 (coiled-coil domain containing 50). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 281.8), Lung (RPKM 277.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ccdc50 in Genome Data Viewer
    Location:
    11q22
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (86837624..86900164, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (73332798..73395333, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (76742179..76804695, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene fibroblast growth factor 12 Neighboring gene uncharacterized LOC134481099 Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC102548576 Neighboring gene uncharacterized LOC102557186

    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
    • 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. Gene knockdown studies revealed CCDC50 as a candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia. Farfsing A, et al. Leukemia, 2009 Nov. PMID 19641524
    2. A mutation in CCDC50, a gene encoding an effector of epidermal growth factor-mediated cell signaling, causes progressive hearing loss. Modamio-Hoybjor S, et al. Am J Hum Genet, 2007 Jun. PMID 17503326, Free PMC Article
    3. Identification and characterization of C3orf6, a new conserved human gene mapping to chromosome 3q28. Vazza G, et al. Gene, 2003 Sep 18. PMID 14527723
    4. The E3 ubiquitin ligases RNF126 and Rabring7 regulate endosomal sorting of the epidermal growth factor receptor. Smith CJ, et al. J Cell Sci, 2013 Mar 15. PMID 23418353
    5. Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis. Na CH, et al. J Proteome Res, 2012 Sep 7. PMID 22871113, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ubiquitin protein ligase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    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
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 50
    Names
    protein Ymer
    putative C3orf6 protein homolog

    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_001401395.1 → NP_001388324.1  coiled-coil domain-containing protein 50 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A0A8I6GF21
      Related
      ENSRNOP00000087350.1, ENSRNOT00000112380.1

    2. NM_182736.2 → NP_877400.1  coiled-coil domain-containing protein 50 isoform 2

      See identical proteins and their annotated locations for NP_877400.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/Swiss-Prot
      Q810U0
      UniProtKB/TrEMBL
      A0A8I6A494
      Related
      ENSRNOP00000085752.1, ENSRNOT00000094418.1
      Conserved Domains (1) summary
      pfam15295
      Location:7 → 126
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    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_086029.1 Reference GRCr8

      Range
      86837624..86900164 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039088104.2 → XP_038944032.1  coiled-coil domain-containing protein 50 isoform X1

      Conserved Domains (1) summary
      pfam15295
      Location:4 → 128
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    RNA

    1. XR_001840408.3 RNA Sequence

    2. XR_010055939.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q810U0.1 GenPept UniProtKB/Swiss-Prot:Q810U0

    Gene LinkOut

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

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