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, ... See more...

Aliases for XIST Gene

Subcategory (RNA class) for XIST Gene


Number of RNA Genes sources:

3 / 17

Aliases for XIST Gene

  • X Inactive Specific Transcript 2 3 5
  • XIST 2 5 165
  • X Inactive Specific Transcript (Non-Protein Coding) 2 3
  • Long Intergenic Non-Protein Coding RNA 1 2 3
  • NCRNA00001 2 3
  • LINC00001 2 3
  • DXS1089 2 3
  • Swd66 2 3
  • X (Inactive)-Specific Transcript (Non-Protein Coding) 2
  • X (Inactive)-Specific Transcript 2
  • NONHSAG054780.2 91
  • HSALNG0138602 164
  • HSALNG0138604 164
  • DXS399E 3
  • SXI1 3

External Ids for XIST Gene

Previous HGNC Symbols for XIST Gene

  • DXS399E

Previous GeneCards Identifiers for XIST Gene

  • GC0XU990236
  • GC0XM071907
  • GC0XM072823
  • GC0XM072957
  • GC0XM066674
  • GC0XM073040

Summaries for XIST Gene

Entrez Gene Summary for XIST Gene

  • 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]

GeneCards Summary for XIST Gene

XIST (X Inactive Specific Transcript) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with XIST include X Inactivation, Familial Skewed, 1 and Hypogonadotropic Hypogonadism.

Gene Wiki entry for XIST Gene

Rfam classification for XIST Gene

  • XIST RNA A repeat
  • X-chromosome inactivation gene exon 1
  • XIST 3' intron conserved motif
  • X-chromosome inactivation gene exon 4

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary and piRNA Summary for XIST Gene

Genomics for XIST Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for XIST Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ073846 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 600.7 +2.8 2799 6.1 SP1 PRDM10 REST ZNF629 ZNF512 SIX5 ZNF692 FOS ZHX2 STAT3 ENSG00000278039 lnc-CHIC1-2 XIST RAB11FIP1P1 JPX FTX DDX3P1 RN7SL648P TOMM20P4 ENSG00000271199
GH0XJ073855 Enhancer 0.7 ENCODE 0.7 -3.0 -2967 0.2 CTCF PRDM10 ZNF692 ZNF174 REST RAD21 TRIM22 ZNF561 RELA ZNF639 XIST lnc-CHIC1-9 CHIC1 ZCCHC13
GH0XJ073841 Enhancer 0.7 Ensembl 0.4 +10.9 10853 2.2 PRDM10 ZNF692 PRDM1 ZNF239 ZNF600 ZBTB20 SP2 ZXDB OSR2 ATF2 JPX ENSG00000228906 piR-50523-001 XIST ENSG00000277577 CHIC1 ZCCHC13
GH0XJ073843 Enhancer 0.6 Ensembl 0.4 +9.3 9253 0.6 ZNF600 ZBTB20 ZXDB BHLHE40 ZNF223 BCL11B SP3 NFRKB ZNF121 PKNOX1 piR-50523-001 piR-50523-002 XIST ENSG00000277577 CHIC1 ZCCHC13
GH0XJ073830 Enhancer 0.7 Ensembl 0.4 +20.9 20853 2.2 PRDM10 ZNF629 ZNF692 ZNF600 ZNF561 MNT ZBTB20 POLR2A OSR2 ZNF580 ENSG00000277577 JPX piR-50523-001 XIST CHIC1 ZCCHC13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around XIST on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the XIST gene promoter:
  • AhR
  • COUP
  • COUP-TF1
  • CUTL1
  • HNF-4alpha1
  • PPAR-gamma1
  • PPAR-gamma2
  • SRY

Genomic Locations for XIST Gene

Genomic Locations for XIST Gene
34,980 bases
Minus strand
32,103 bases
Minus strand

Genomic View for XIST Gene

Genes around XIST on UCSC Golden Path with GeneCards custom track
XIST in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
XIST Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XIST Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XIST Gene

Proteins for XIST Gene

Post-translational modifications for XIST Gene

No Post-translational modifications

No data available for DME Specific Peptides for XIST Gene

Domains & Families for XIST Gene

Gene Families for XIST Gene

genes like me logo Genes that share domains with XIST: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for XIST Gene

Function for XIST Gene

Molecular function for XIST Gene

GENATLAS Biochemistry:
X inactive,specific transcript,implicated in recognizing the number of X chromosomes and initiating a silencing signal on cis,with promoter mutation in extreme skewed X inactivation pattern,replicated before its expressed allele,involved in the overexpression of H2A1M in inactivated X
genes like me logo Genes that share phenotypes with XIST: view

Human Phenotype Ontology for XIST Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for XIST Gene

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for XIST Gene

Localization for XIST Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XIST gene
Compartment Confidence
nucleus 3
extracellular 2
cytoskeleton 2
mitochondrion 2
cytosol 2
plasma membrane 1
endoplasmic reticulum 1
endosome 1
lysosome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for XIST Gene

Pathways & Interactions for XIST Gene

PathCards logo

SuperPathways for XIST Gene

No Data Available

Gene Ontology (GO) - Biological Process for XIST Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009048 dosage compensation by inactivation of X chromosome IEA --
GO:0016458 gene silencing IEA --
genes like me logo Genes that share ontologies with XIST: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for XIST Gene

Drugs & Compounds for XIST Gene

No Compound Related Data Available

Transcripts for XIST Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for XIST Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS00000BB971_9606 lncRNA 724 4

Ensembl: ENST00000417942 (view in UCSC) ,

LncBook: HSALNT0283650,

LNCipedia: XIST:25,


URS00002EE2B5_9606 lncRNA 583 4

Ensembl: ENST00000602587 (view in UCSC) ,

LncBook: HSALNT0283656,

LNCipedia: XIST:18,


URS000075D95B_9606 lncRNA 19280 2

HGNC: 12810,

RefSeq: NR_001564,

URS00000E70EF_9606 lncRNA 827 2

Ensembl: ENST00000602495 (view in UCSC) ,

LNCipedia: XIST:16,

URS0000DB8B87_9606 lncRNA 19245 1

Ensembl: ENST00000429829 (view in UCSC) ,

XIST in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for XIST Gene

11 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for XIST Gene

No ASD Table

Relevant External Links for XIST Gene

GeneLoc Exon Structure for

Expression for XIST Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for XIST Gene

mRNA differential expression in normal tissues according to GTEx for XIST Gene

This gene is overexpressed in Ovary (x4.8).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for XIST

SOURCE GeneReport for Unigene cluster for XIST Gene:


Evidence on tissue expression from TISSUES for XIST Gene

  • Skin(2.4)
  • Nervous system(2.2)
  • Blood(2.2)
genes like me logo Genes that share expression patterns with XIST: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for XIST Gene

Orthologs for XIST Gene

Evolution for XIST Gene

Gene Tree for XIST (if available)
Gene Tree for XIST (if available)

No data available for Orthologs for XIST Gene

Paralogs for XIST Gene

No data available for Paralogs for XIST Gene

Variants for XIST Gene

Additional dbSNP identifiers (rs#s) for XIST Gene

Additional Variant Information for XIST Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP , Structural Variations from Database of Genomic Variants (DGV) and Variation tolerance for XIST Gene

Disorders for XIST Gene

MalaCards: The human disease database

(29) MalaCards diseases for XIST Gene - From: LncRNADisease, ClinVar, GTR, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
x inactivation, familial skewed, 1
  • sxi1
hypogonadotropic hypogonadism
  • congenital idiopathic hypogonadotropic hypogonadism
collecting duct carcinoma
  • bdc
testicular germ cell cancer
  • testicular germ cell tumor
microinvasive gastric cancer
  • early gastric cancer
- elite association - COSMIC cancer census association via MalaCards
Search XIST in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with XIST: view

No data available for UniProtKB/Swiss-Prot and Genatlas for XIST Gene

Publications for XIST Gene

  1. Inducible XIST-dependent X-chromosome inactivation in human somatic cells is reversible. (PMID: 17537922) Chow JC … Brown CJ (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 23
  2. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. (PMID: 16778056) Duret L … Avner P (Science (New York, N.Y.) 2006) 2 3
  3. Familial cases of point mutations in the XIST promoter reveal a correlation between CTCF binding and pre-emptive choices of X chromosome inactivation. (PMID: 15731119) Pugacheva EM … Lobanenkov VV (Human molecular genetics 2005) 3 23
  4. A revision of the human XIST gene organization and structural comparison with mouse Xist. (PMID: 10723727) Hong YK … Strauss WM (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 3 23
  5. A promoter mutation in the XIST gene in two unrelated families with skewed X-chromosome inactivation. (PMID: 9354806) Plenge RM … Willard HF (Nature genetics 1997) 3 23

Products for XIST Gene

Sources for XIST Gene