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

Gene ID: 72997, updated on 16-Mar-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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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. The Vertebrate Genome Annotation browser 10 years on. Harrow JL, et al. Nucleic Acids Res, 2014 Jan. PMID 24316575, Free PMC Article
  5. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article

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)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (1) 

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

Gene LinkOut

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