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

Gene ID: 67501, updated on 2-Nov-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, Nov 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 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 (32) 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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