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    6820408C15Rik RIKEN cDNA 6820408C15 gene [ Mus musculus (house mouse) ]

    Gene ID: 228778, updated on 27-Nov-2024

    Summary

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    Official Symbol
    6820408C15Rikprovided by MGI
    Official Full Name
    RIKEN cDNA 6820408C15 geneprovided by MGI
    Primary source
    MGI:MGI:3045333
    See related
    Ensembl:ENSMUSG00000032680 AllianceGenome:MGI:3045333
    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
    Summary
    Orthologous to human C20orf96 (chromosome 20 open reading frame 96). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 7.1), lung adult (RPKM 0.9) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See 6820408C15Rik in Genome Data Viewer
    Location:
    2 H1; 2 74.99 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (152257507..152286256)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (152415587..152444336)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene VISTA enhancer mm271 Neighboring gene SRY (sex determining region Y)-box 12 Neighboring gene STARR-positive B cell enhancer mm9_chr2:152231818-152232119 Neighboring gene zinc finger, CCHC domain containing 3 Neighboring gene predicted gene, 27343 Neighboring gene predicted gene, 39960 Neighboring gene defensin beta 23

    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. Tissue expression patterns identify mouse cilia genes. McClintock TS, et al. Physiol Genomics, 2008 Jan 17. PMID 17971504
    2. The sperm-associated antigen 6 interactome and its role in spermatogenesis. Liu Y, et al. Reproduction, 2019 Aug. PMID 31146259, Free PMC Article
    3. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. Magdaleno S, et al. PLoS Biol, 2006 Apr. PMID 16602821, Free PMC Article
    4. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, Free PMC Article
    5. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • RP23-453K8.1

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    uncharacterized protein C20orf96 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_001289738.1 → NP_001276667.1  uncharacterized protein C20orf96 homolog isoform 1

      See identical proteins and their annotated locations for NP_001276667.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK078482, AW048149, BC137826
      UniProtKB/TrEMBL
      B2RQ99
      Conserved Domains (1) summary
      pfam15397
      Location:97 → 354
      DUF4618; Domain of unknown function (DUF4618)

    2. NM_001379452.1 → NP_001366381.1  uncharacterized protein C20orf96 homolog isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL844517
      Conserved Domains (1) summary
      pfam15397
      Location:27 → 284
      DUF4618; Domain of unknown function (DUF4618)

    3. NM_177656.4 → NP_808324.1  uncharacterized protein C20orf96 homolog isoform 2

      See identical proteins and their annotated locations for NP_808324.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK078482, AW048149
      Consensus CDS
      CCDS16885.1
      UniProtKB/TrEMBL
      Q8BJX2
      Related
      ENSMUSP00000037024.6, ENSMUST00000039961.12
      Conserved Domains (1) summary
      pfam15397
      Location:97 → 353
      DUF4618; Domain of unknown function (DUF4618)

    RNA

    1. NR_110367.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses alternate splice sites in two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK078482, AW048149, BC144943

    2. NR_110368.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an internal exon and uses alternate splice sites in two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK078482, AW048149, BC144943

    3. NR_166674.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL844517

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      152257507..152286256
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011239479.3 → XP_011237781.1  uncharacterized protein C20orf96 homolog isoform X1

      See identical proteins and their annotated locations for XP_011237781.1

      UniProtKB/TrEMBL
      B2RQ99
      Conserved Domains (1) summary
      pfam15397
      Location:97 → 354
      DUF4618; Domain of unknown function (DUF4618)

    2. XM_011239480.3 → XP_011237782.1  uncharacterized protein C20orf96 homolog isoform X2

      See identical proteins and their annotated locations for XP_011237782.1

      UniProtKB/TrEMBL
      Q8BJX2
      Conserved Domains (1) summary
      pfam15397
      Location:97 → 353
      DUF4618; Domain of unknown function (DUF4618)

    3. XM_036161464.1 → XP_036017357.1  uncharacterized protein C20orf96 homolog isoform X3

      Conserved Domains (1) summary
      pfam15397
      Location:2 → 259
      DUF4618; Domain of unknown function (DUF4618)

    4. XM_036161465.1 → XP_036017358.1  uncharacterized protein C20orf96 homolog isoform X4

      Conserved Domains (1) summary
      pfam15397
      Location:56 → 229
      DUF4618; Domain of unknown function (DUF4618)

    5. XM_036161463.1 → XP_036017356.1  uncharacterized protein C20orf96 homolog isoform X1

      UniProtKB/TrEMBL
      B2RQ99
      Conserved Domains (1) summary
      pfam15397
      Location:97 → 354
      DUF4618; Domain of unknown function (DUF4618)

    RNA

    1. XR_004940123.1 RNA Sequence

    2. XR_004940122.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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