U.S. flag

An official website of the United States government

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

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

Summary

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

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

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

General gene information

Other Names

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

Clone Names

  • DKFZp779P0129

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in X chromosome PubMed 
part_of dosage compensation complex PubMed 
part_of ribonucleoprotein complex PubMed 

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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)
External link. Please review our privacy policy.