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    Xist inactive X specific transcripts [ Mus musculus (house mouse) ]

    Gene ID: 213742, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Xistprovided by MGI
    Official Full Name
    inactive X specific transcriptsprovided by MGI
    Primary source
    MGI:MGI:98974
    See related
    Ensembl:ENSMUSG00000086503 AllianceGenome:MGI:98974
    Gene type
    ncRNA
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    A430022B11
    Summary
    X inactivation is an early developmental process in mammalian females that transcriptionally silences one of the pair of X chromosomes, thus providing dosage equivalence between males and females. The process is regulated by several factors, including a region of chromosome X called the X inactivation center (XIC). The XIC comprises several non-coding and protein-coding genes, and this gene was the first non-coding gene identified within the XIC. This gene is expressed exclusively from the XIC of the inactive X chromosome. It is essential for the initiation and spread of X-inactivation. It silences hundreds of genes by recruiting and tethering repressive chromatin-modifying complexes to the inactive X chromosome. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Apr 2012]
    Expression
    Broad expression in limb E14.5 (RPKM 75.7), CNS E11.5 (RPKM 39.9) and 19 other tissues See more
    Orthologs
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    Genomic context

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    See Xist in Genome Data Viewer
    Location:
    X D; X 46.15 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (102503979..102526839, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (103460373..103483233, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_47688 Neighboring gene predicted gene 9516 Neighboring gene cysteine-rich hydrophobic domain 1 Neighboring gene testis specific X-linked gene Neighboring gene STARR-seq mESC enhancer starr_47691 Neighboring gene origin of replication in Tsix Neighboring gene X (inactive)-specific transcript, opposite strand Neighboring gene origin of replication in exon 1 of Xist Neighboring gene ribosomal protein S12, pseudogene 1 Neighboring gene predicted gene 14861

    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. Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X. Colognori D, et al. Mol Cell, 2019 Apr 4. PMID 30827740, Free PMC Article
    2. Attenuated spread of X-inactivation in an X;autosome translocation. Popova BC, et al. Proc Natl Acad Sci U S A, 2006 May 16. PMID 16679409, Free PMC Article
    3. Exit from Naive Pluripotency Induces a Transient X Chromosome Inactivation-like State in Males. Sousa EJ, et al. Cell Stem Cell, 2018 Jun 1. PMID 29804891, Free PMC Article
    4. A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Sun BK, et al. Mol Cell, 2006 Mar 3. PMID 16507360
    5. Analysis of the Xist RNA isoforms suggests two distinctly different forms of regulation. Ma M, et al. Mamm Genome, 2005 Jun. PMID 16075366

    See all (383) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation.
      Title: G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation.
    2. YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing.
      Title: YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing.
    3. Long noncoding RNA XIST inhibition promotes Leydig cell apoptosis by acting as a competing endogenous RNA for microRNA-145a-5p that targets SIRT1 in late-onset hypogonadism.
      Title: Long noncoding RNA XIST inhibition promotes Leydig cell apoptosis by acting as a competing endogenous RNA for microRNA-145a-5p that targets SIRT1 in late-onset hypogonadism.
    4. Xist ribonucleoproteins promote female sex-biased autoimmunity.
      Title: Xist ribonucleoproteins promote female sex-biased autoimmunity.
    5. Gender dimorphism in hepatocarcinogenesis-DNA methylation modification regulated X-chromosome inactivation escape molecule XIST.
      Title: Gender dimorphism in hepatocarcinogenesis-DNA methylation modification regulated X-chromosome inactivation escape molecule XIST.
    6. GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers.
      Title: GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers.
    7. IncRNA XIST Promotes Cardiac Fibrosis in Mice with Diabetic Nephropathy via Sponging miR-106a-5p to Target RUNX1.
      Title: IncRNA XIST Promotes Cardiac Fibrosis in Mice with Diabetic Nephropathy via Sponging miR-106a-5p to Target RUNX1.
    8. LncRNA XIST promotes mitochondrial dysfunction of hepatocytes to aggravate hepatic fibrogenesis via miR-539-3p/ADAMTS5 axis.
      Title: LncRNA XIST promotes mitochondrial dysfunction of hepatocytes to aggravate hepatic fibrogenesis via miR-539-3p/ADAMTS5 axis.
    9. XIST silencing alleviated inflammation and mesangial cells proliferation in diabetic nephropathy by sponging miR-485.
      Title: XIST silencing alleviated inflammation and mesangial cells proliferation in diabetic nephropathy by sponging miR-485.
    10. Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism.
      Title: Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism.
    Submit: New GeneRIF Correction See all GeneRIFs (142)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (26)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ribonucleoprotein complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within inactivation of paternal X chromosome by genomic imprinting IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within inactivation of paternal X chromosome by genomic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within random inactivation of X chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within random inactivation of X chromosome IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within spongiotrophoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in X chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    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_001463.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AL669964
      Related
      ENSMUST00000127786.4

    2. NR_001570.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is alternatively spliced in the 3' end and is shorter compared to variant 1.
      Source sequence(s)
      AL669964

    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
      102503979..102526839 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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