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    Silc1 sciatic injury induced lincRNA upregulator of SOX11 [ Mus musculus (house mouse) ]

    Gene ID: 636791, updated on 8-Feb-2024

    Summary

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    Official Symbol
    Silc1provided by MGI
    Official Full Name
    sciatic injury induced lincRNA upregulator of SOX11provided by MGI
    Primary source
    MGI:MGI:3643118
    See related
    Ensembl:ENSMUSG00000094002 AllianceGenome:MGI:3643118
    Gene type
    ncRNA
    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
    Gm9866; EG636791
    Summary
    Orthologous to human SILC1 (sciatic injury induced lincRNA upregulator of SOX11). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in cortex adult (RPKM 5.1), cerebellum adult (RPKM 3.7) and 5 other tissues See more
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    Genomic context

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    See Silc1 in Genome Data Viewer
    Location:
    12 A2; 12 9.86 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (27190795..27210515, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (27140796..27160516, complement)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 30515 Neighboring gene VISTA enhancer mm1609 Neighboring gene STARR-seq mESC enhancer starr_31795 Neighboring gene STARR-seq mESC enhancer starr_31796 Neighboring gene predicted gene, 30401 Neighboring gene predicted gene, 20187 Neighboring gene STARR-seq mESC enhancer starr_31800 Neighboring gene predicted gene, 40872 Neighboring gene predicted gene, 52005

    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. Regulation of Neuroregeneration by Long Noncoding RNAs. Perry RB, et al. Mol Cell, 2018 Nov 1. PMID 30401432, Free PMC Article
    2. The Vertebrate Genome Annotation browser 10 years on. Harrow JL, et al. Nucleic Acids Res, 2014 Jan. PMID 24316575, Free PMC Article
    3. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article
    4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    5. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA-Gm9866 promotes liver fibrosis by activating TGFbeta/Smad signaling via targeting Fam98b.
      Title: LncRNA-Gm9866 promotes liver fibrosis by activating TGFβ/Smad signaling via targeting Fam98b.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

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    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
    		  

    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.

    RNA

    1. NR_045868.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC155270, AK163447
      Related
      ENSMUST00000182473.3

    2. NR_045869.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site and lacks an internal exon in the 3' region, compared to variant 1.
      Source sequence(s)
      AC155270, AK163447, BY128170, BY243558
      Related
      ENSMUST00000245682.1

    3. NR_045870.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two consecutive internal exons, compared to variant 1.
      Source sequence(s)
      AC155270, AK163447, BE648300

    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_000078.7 Reference GRCm39 C57BL/6J

      Range
      27190795..27210515 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001039248.1: Suppressed sequence

      Description
      NM_001039248.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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