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

Gene ID: 636791, updated on 2-Nov-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, Nov 2024]
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 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. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation. Ben-Tov Perry R, et al. Cell Rep, 2023 Oct 31. PMID 37742186, Free PMC Article
  2. LncRNA-Gm9866 promotes liver fibrosis by activating TGFβ/Smad signaling via targeting Fam98b. Liao X, et al. J Transl Med, 2023 Nov 2. PMID 37919785, Free PMC Article
  3. Regulation of Neuroregeneration by Long Noncoding RNAs. Perry RB, et al. Mol Cell, 2018 Nov 1. PMID 30401432, Free PMC Article
  4. The Vertebrate Genome Annotation browser 10 years on. Harrow JL, et al. Nucleic Acids Res, 2014 Jan. PMID 24316575, Free PMC Article
  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 (13) 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
    ENSMUST00000182473.4

  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
    ENSMUST00000245682.2

  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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