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

Gene ID: 7503, updated on 24-Mar-2024


Official Symbol
XISTprovided by HGNC
Official Full Name
X inactive specific transcriptprovided by HGNC
Primary source
See related
Ensembl:ENSG00000229807 MIM:314670; AllianceGenome:HGNC:12810
Gene type
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SXI1; swd66; DXS1089; DXS399E; LINC00001; NCRNA00001
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]
Broad expression in thyroid (RPKM 59.4), ovary (RPKM 51.4) and 20 other tissues See more
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Genomic context

Exon count:
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (73820651..73852753, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (72253967..72286069, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (73040486..73072588, 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


  • 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


GeneRIFs: Gene References Into Functions

What's a GeneRIF?


Associated conditions

Description Tests
X inactivation, familial skewed, 1
MedGen: C1848138 OMIM: 300087 GeneReviews: Not available
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Copy number response

Copy number response

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

ClinGen Genome Curation Page

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

ClinGen Genome Curation PagePubMed


Products Interactant Other Gene Complex Source Pubs Description

General gene information


Other Names

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

Clone Names

  • DKFZp779P0129

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.


  1. NG_016172.1 RefSeqGene

    GenBank, FASTA, Sequence Viewer (Graphics)


  1. NR_001564.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AI640908, AL353804, BX648323

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly


  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    73820651..73852753 complement
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0


  1. NC_060947.1 Alternate T2T-CHM13v2.0

    72253967..72286069 complement
    GenBank, FASTA, Sequence Viewer (Graphics)