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    Kantr Kdm5c adjacent non-coding transcript [ Mus musculus (house mouse) ]

    Gene ID: 72997, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Kantrprovided by MGI
    Official Full Name
    Kdm5c adjacent non-coding transcriptprovided by MGI
    Primary source
    MGI:MGI:1920247
    See related
    Ensembl:ENSMUSG00000087403 AllianceGenome:MGI:1920247
    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
    Spasm; 2810454L23Rik; 2900056M20Rik
    Summary
    This gene is thought to produce a functional long non-coding RNA. Mutation of this locus causes tremors and spastic movements, suggesting a role for this gene in neurological development or function. [provided by RefSeq, Feb 2015]
    Expression
    Broad expression in CNS E18 (RPKM 8.0), whole brain E14.5 (RPKM 7.1) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Kantr in Genome Data Viewer
    Location:
    X F3; X 68.46 cM
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (151077820..151110489, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (152294824..152327493, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain 2 Neighboring gene STARR-seq mESC enhancer starr_48090 Neighboring gene predicted gene, 52430 Neighboring gene STARR-seq mESC enhancer starr_48091 Neighboring gene lysine demethylase 5C Neighboring gene STARR-seq mESC enhancer starr_48092 Neighboring gene STARR-seq mESC enhancer starr_48093 Neighboring gene STARR-positive B cell enhancer mm9_chrX:148771022-148771323 Neighboring gene TSPY-like 2 Neighboring gene RIKEN cDNA 3010001F23 gene Neighboring gene G-protein coupled receptor 173

    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. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Goff LA, et al. Proc Natl Acad Sci U S A, 2015 Jun 2. PMID 26034286, Free PMC Article
    2. Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs. Lai KM, et al. PLoS One, 2015. PMID 25909911, Free PMC Article
    3. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Sauvageau M, et al. Elife, 2013 Dec 31. PMID 24381249, Free PMC Article
    4. USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and noncatalytic activities. Liu C, et al. Sci Adv, 2023 May 19. PMID 37196079, Free PMC Article
    5. The Vertebrate Genome Annotation browser 10 years on. Harrow JL, et al. Nucleic Acids Res, 2014 Jan. PMID 24316575, Free PMC Article

    See all (15) 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) 
    • Targeted (1)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    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_040269.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC083816, AW213569, BY001618

    2. NR_040270.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' terminal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC083816, BB852892, BY001618, BY201328
      Related
      ENSMUST00000195280.3

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      151077820..151110489 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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