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    Ccdc50 coiled-coil domain containing 50 [ Mus musculus (house mouse) ]

    Gene ID: 67501, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ccdc50provided by MGI
    Official Full Name
    coiled-coil domain containing 50provided by MGI
    Primary source
    MGI:MGI:1914751
    See related
    Ensembl:ENSMUSG00000038127 AllianceGenome:MGI:1914751
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    C3orf6
    Summary
    Predicted to enable ubiquitin protein ligase binding activity. Predicted to act upstream of or within sensory perception of sound. Located in microtubule cytoskeleton. Is expressed in several structures, including brain; cochlear ganglion; gonad; hemolymphoid system gland; and inner ear. 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, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 15.7), CNS E14 (RPKM 15.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ccdc50 in Genome Data Viewer
    Location:
    16 B2; 16 18.98 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (27205815..27270968)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (27387065..27452218)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr16:27349423-27349723 Neighboring gene osteocrin Neighboring gene voltage-dependent anion channel 3 pseudogene Neighboring gene STARR-positive B cell enhancer mm9_chr16:27388391-27388692 Neighboring gene urotensin 2B Neighboring gene STARR-seq mESC enhancer starr_40496 Neighboring gene predicted gene, 32356 Neighboring gene STARR-seq mESC enhancer starr_40498 Neighboring gene predicted gene, 53942

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The regulation of NLRP3 inflammasome activation by CCDC50-mediated autophagy. Hou P, et al. Autophagy, 2023 Jan. PMID 35620989, Free PMC Article
    2. Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants. Lachgar-Ruiz M, et al. Dis Model Mech, 2023 Aug 1. PMID 37165931, Free PMC Article
    3. Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases. Hou P, et al. Cell Mol Immunol, 2021 Oct. PMID 34453126, Free PMC Article
    4. Identification and characterization of C3orf6, a new conserved human gene mapping to chromosome 3q28. Vazza G, et al. Gene, 2003 Sep 18. PMID 14527723
    5. 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

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants.
      Title: Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants.
    2. The regulation of NLRP3 inflammasome activation by CCDC50-mediated autophagy.
      Title: The regulation of NLRP3 inflammasome activation by CCDC50-mediated autophagy.
    3. Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases.
      Title: Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases.
    4. Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth.
      Title: Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2)  1 citation
    • Targeted (2) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • 2610529H08Rik, 5730448P06Rik

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ubiquitin protein ligase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 50
    Names
    protein Ymer

    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_001025615.3 → NP_001020786.1  coiled-coil domain-containing protein 50 isoform 2

      See identical proteins and their annotated locations for NP_001020786.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AK147820, AK151672, AK162970, AK166690, BE948353, CA319864, CF734428, CJ045424
      Consensus CDS
      CCDS37306.1
      UniProtKB/TrEMBL
      Q3TNK7
      Related
      ENSMUSP00000093841.5, ENSMUST00000096127.11
      Conserved Domains (1) summary
      pfam15295
      Location:7 → 126
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    2. NM_001289436.1 → NP_001276365.1  coiled-coil domain-containing protein 50 isoform 3

      See identical proteins and their annotated locations for NP_001276365.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK147820, AK151672, AK162970, AK166690, BE948353, CA319864, CF734428, CJ045424, CT010568
      UniProtKB/Swiss-Prot
      Q810U5

    3. NM_026202.4 → NP_080478.2  coiled-coil domain-containing protein 50 isoform 1

      See identical proteins and their annotated locations for NP_080478.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK147820, AK151672, AK162970, AK166690, BE948353, CA319864, CF734428, CJ045424
      Consensus CDS
      CCDS37305.1
      UniProtKB/Swiss-Prot
      A6X929, Q3TRW1, Q810U5, Q8BP82, Q9CZT1, Q9D436
      UniProtKB/TrEMBL
      A6H6M8
      Related
      ENSMUSP00000097604.4, ENSMUST00000100026.10
      Conserved Domains (1) summary
      pfam15295
      Location:4 → 128
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      27205815..27270968
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011246002.3 → XP_011244304.1  coiled-coil domain-containing protein 50 isoform X3

      UniProtKB/TrEMBL
      A0A668KL36
      Related
      ENSMUSP00000159204.2, ENSMUST00000239351.2
      Conserved Domains (1) summary
      pfam15295
      Location:4 → 128
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    2. XM_006522483.3 → XP_006522546.1  coiled-coil domain-containing protein 50 isoform X1

      UniProtKB/TrEMBL
      F6UK66
      Conserved Domains (1) summary
      pfam15295
      Location:6 → 116
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus

    3. XM_030249249.2 → XP_030105109.1  coiled-coil domain-containing protein 50 isoform X2

      UniProtKB/TrEMBL
      F6UK66
      Conserved Domains (1) summary
      pfam15295
      Location:6 → 116
      CCDC50_N; Coiled-coil domain-containing protein 50 N-terminus
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q810U5.1 GenPept UniProtKB/Swiss-Prot:Q810U5

    Gene LinkOut

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

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