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    XIST X inactive specific transcript [ Homo sapiens (human) ]

    Gene ID: 7503, updated on 10-Dec-2024

    Summary

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    Official Symbol
    XISTprovided by HGNC
    Official Full Name
    X inactive specific transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:12810
    See related
    Ensembl:ENSG00000229807 MIM:314670; AllianceGenome:HGNC:12810
    Gene type
    ncRNA
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SXI1; swd66; DXS1089; DXS399E; LINC00001; NCRNA00001
    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, and is essential for the initiation and spread of X-inactivation. The transcript is a spliced RNA. Alternatively spliced transcript variants have been identified, but their full length sequences have not been determined. Mutations in the XIST promoter cause familial skewed X inactivation. [provided by RefSeq, Apr 2012]
    Expression
    Broad expression in thyroid (RPKM 59.4), ovary (RPKM 51.4) and 20 other tissues See more
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    Genomic context

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    See XIST in Genome Data Viewer
    Location:
    Xq13.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (73820656..73852714, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (72253972..72286030, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (73040491..73072549, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20905 Neighboring gene cysteine rich hydrophobic domain 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:72891741-72891916 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:72948368-72948916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:72987649-72988534 Neighboring gene NANOG hESC enhancer GRCh37_chrX:73005301-73006000 Neighboring gene selenophosphate synthetase 1 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29763 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:73071267-73071768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:73083465-73084112 Neighboring gene TSIX transcript, XIST antisense RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:73134838-73135338 Neighboring gene FXYD domain containing ion transport regulator 6 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29765 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:73185196-73185760 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:73186327-73186890 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:73197425-73197984 Neighboring gene JPX transcript, XIST activator Neighboring gene ribosomal protein SA pseudogene 14 Neighboring gene FTX transcript, XIST regulator

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements. Lee HJ, et al. Nucleic Acids Res, 2019 May 7. PMID 30783652, Free PMC Article
    2. LncRNA XIST serves as a ceRNA to regulate the expression of ASF1A, BRWD1M, and PFKFB2 in kidney transplant acute kidney injury via sponging hsa-miR-212-3p and hsa-miR-122-5p. Cheng Q, et al. Cell Cycle, 2020 Feb. PMID 31914881, Free PMC Article
    3. Downregulation of LncRNA-XIST inhibited development of non-small cell lung cancer by activating miR-335/SOD2/ROS signal pathway mediated pyroptotic cell death. Liu J, et al. Aging (Albany NY), 2019 Sep 25. PMID 31553952, Free PMC Article
    4. The suppression of ox-LDL-induced inflammatory response and apoptosis of HUVEC by lncRNA XIAT knockdown via regulating miR-30c-5p/PTEN axis. Hu WN, et al. Eur Rev Med Pharmacol Sci, 2019 Sep. PMID 31539155
    5. Long Non-coding RNA XIST May Influence Cervical Ossification of the Posterior Longitudinal Ligament Through Regulation of miR-17-5P/AHNAK/BMP2 Signaling Pathway. Liao X, et al. Calcif Tissue Int, 2019 Dec. PMID 31511959

    See all (264) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Trisomy silencing by XIST: translational prospects and challenges.
      Title: Trisomy silencing by XIST: translational prospects and challenges.
    2. XIST and MUC1-C form an auto-regulatory pathway in driving cancer progression.
      Title: XIST and MUC1-C form an auto-regulatory pathway in driving cancer progression.
    3. lncRNA XIST Interacts with Regulatory T Cells within the Tumor Microenvironment in Chronic Hepatitis B-Associated Hepatocellular Carcinoma.
      Title: lncRNA XIST Interacts with Regulatory T Cells within the Tumor Microenvironment in Chronic Hepatitis B-Associated Hepatocellular Carcinoma.
    4. Long Non-coding RNA X-Inactive Specific Transcript Promotes Esophageal Squamous Cell Carcinoma Progression via the MicroRNA 34a/Zinc Finger E-box-Binding Homeobox 1 Pathway.
      Title: Long Non-coding RNA X-Inactive Specific Transcript Promotes Esophageal Squamous Cell Carcinoma Progression via the MicroRNA 34a/Zinc Finger E-box-Binding Homeobox 1 Pathway.
    5. Discovering therapeutic possibilities for polycystic ovary syndrome by targeting XIST and its associated ceRNA network through the analysis of transcriptome data.
      Title: Discovering therapeutic possibilities for polycystic ovary syndrome by targeting XIST and its associated ceRNA network through the analysis of transcriptome data.
    6. 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.
    7. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.
      Title: Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.
    8. Exploring the XIST axis as oxidative stress-related signatures in systemic lupus erythematosus.
      Title: Exploring the XIST axis as oxidative stress-related signatures in systemic lupus erythematosus.
    9. METTL14-mediated lncRNA XIST silencing alleviates GDM progression by facilitating trophoblast cell proliferation and migration via the miR-497-5p/FOXO1 axis.
      Title: METTL14-mediated lncRNA XIST silencing alleviates GDM progression by facilitating trophoblast cell proliferation and migration via the miR-497-5p/FOXO1 axis.
    10. Long noncoding RNA X-inactive specific transcript (lncRNA XIST) inhibits hepatic insulin resistance by competitively binding microRNA-182-5p.
      Title: Long noncoding RNA X-inactive specific transcript (lncRNA XIST) inhibits hepatic insulin resistance by competitively binding microRNA-182-5p.
    Submit: New GeneRIF Correction See all GeneRIFs (233)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    X inactivation, familial skewed, 1
    MedGen: C1848138 OMIM: 300087 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-04-22)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-04-22)

    ClinGen Genome Curation PagePubMed

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

    • X inactive specific transcript (non-protein coding)
    • long intergenic non-protein coding RNA 1

    Clone Names

    • DKFZp779P0129

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin-protein adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables miRNA inhibitor activity via base-pairing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in constitutive heterochromatin formation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in lncRNA-mediated post-transcriptional gene silencing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of miRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in random inactivation of X chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in random inactivation of X chromosome IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in random inactivation of X chromosome TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulatory ncRNA-mediated heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in X chromosome TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of dosage compensation complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of ribonucleoprotein complex 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.

    Genomic

    1. NG_016172.1 RefSeqGene

      Range
      5001..37103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. NR_001564.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804
      Related
      ENST00000429829.6

    2. NR_190997.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804
      Related
      ENST00000650627.1

    3. NR_190998.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    4. NR_190999.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    5. NR_191000.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    6. NR_191001.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    7. NR_191002.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    8. NR_191003.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    9. NR_191004.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    10. NR_191005.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    11. NR_191006.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    12. NR_191007.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    13. NR_191009.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL353804

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      73820656..73852714 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      72253972..72286030 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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    Chemical Information
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    Research Materials