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    6030458C11Rik RIKEN cDNA 6030458C11 gene [ Mus musculus (house mouse) ]

    Gene ID: 77877, updated on 5-Mar-2024

    Summary

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    Official Symbol
    6030458C11Rikprovided by MGI
    Official Full Name
    RIKEN cDNA 6030458C11 geneprovided by MGI
    Primary source
    MGI:MGI:1925127
    See related
    Ensembl:ENSMUSG00000022195 AllianceGenome:MGI:1925127
    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 C5orf22 (chromosome 5 open reading frame 22). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in liver E14 (RPKM 7.9), liver E14.5 (RPKM 7.7) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    15 A1; 15 5.98 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (12806012..12824767, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (12808177..12824679, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 17756 Neighboring gene STARR-positive B cell enhancer ABC_E4128 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:12754551-12754660 Neighboring gene CapStarr-seq enhancer MGSCv37_chr15:12754713-12754896 Neighboring gene predicted gene, 41274 Neighboring gene STARR-seq mESC enhancer starr_38037 Neighboring gene drosha, ribonuclease type III Neighboring gene STARR-seq mESC enhancer starr_38041 Neighboring gene STARR-seq mESC enhancer starr_38042 Neighboring gene cadherin 6 Neighboring gene STARR-seq mESC enhancer starr_38043 Neighboring gene predicted gene, 35018

    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. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Carninci P, et al. Genome Res, 2003 Jun. PMID 12819125, Free PMC Article
    2. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    3. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
    4. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (16) 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) 

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC118638

    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
    UPF0489 protein C5orf22 homolog

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001166360.2 → NP_001159832.1  UPF0489 protein C5orf22 homolog isoform a

      See identical proteins and their annotated locations for NP_001159832.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) contains a distinct 3' UTR and lacks most of the 3' coding region, compared to variant 1. These differences result in a protein (isoform a) with a shorter C-terminus, compared to isoform b.
      Source sequence(s)
      AC133189
      UniProtKB/Swiss-Prot
      Q8BGC1
      Related
      ENSMUST00000228888.2
      Conserved Domains (1) summary
      pfam12640
      Location:19 → 104
      UPF0489; UPF0489 domain

    2. NM_001357761.2 → NP_001344690.1  UPF0489 protein C5orf22 homolog isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region and uses a downstream start codon compared to variant 2. It encodes isoform c which has a shorter N-terminus compared to isoform b.
      Source sequence(s)
      AC133189
      Consensus CDS
      CCDS88737.1
      UniProtKB/TrEMBL
      A0A2I3BRJ4
      Related
      ENSMUSP00000154605.2, ENSMUST00000227299.2
      Conserved Domains (1) summary
      pfam12640
      Location:1 → 95
      UPF0489; UPF0489 domain

    3. NM_029998.4 → NP_084274.1  UPF0489 protein C5orf22 homolog isoform b

      See identical proteins and their annotated locations for NP_084274.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (b).
      Source sequence(s)
      AC133189
      Consensus CDS
      CCDS27392.1
      UniProtKB/Swiss-Prot
      B2RQ49, Q8BGC1, Q8BYV3, Q8BZ46, Q9CX64
      Related
      ENSMUSP00000055656.4, ENSMUST00000057256.5
      Conserved Domains (1) summary
      pfam12640
      Location:19 → 169
      UPF0489; UPF0489 domain

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      12806012..12824767 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036159632.1 → XP_036015525.1  UPF0489 protein C5orf22 homolog isoform X1

      Conserved Domains (1) summary
      pfam12640
      Location:19 → 169
      UPF0489; UPF0489 domain

    2. XM_036159633.1 → XP_036015526.1  UPF0489 protein C5orf22 homolog isoform X2

      Conserved Domains (1) summary
      pfam12640
      Location:19 → 169
      UPF0489; UPF0489 domain

    RNA

    1. XR_004938878.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BGC1.1 GenPept UniProtKB/Swiss-Prot:Q8BGC1

    Gene LinkOut

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

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