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

Gene ID: 228778, updated on 5-Mar-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, Apr 2022]
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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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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