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Aliases for XIST Gene

Subcategory (RNA class) for XIST Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for XIST Gene

  • X Inactive Specific Transcript 2 3
  • X Inactive Specific Transcript (Non-Protein Coding) 2 3 5
  • Long Intergenic Non-Protein Coding RNA 1 2 3
  • X (Inactive)-Specific Transcript (Non-Protein Coding) 2
  • X (Inactive)-Specific Transcript 2
  • NCRNA00001 3
  • LINC00001 3
  • DXS1089 3
  • DXS399E 3
  • Swd66 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 non-coding RNA class. Diseases associated with XIST include X Inactivation, Familial Skewed, 1 and Hypogonadotropic Hypogonadism.

Gene Wiki entry for XIST Gene

Additional gene information for XIST Gene

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

Genomics for XIST Gene

GeneHancer (GH) Regulatory Elements for XIST Gene

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
GH0XJ073849 Promoter/Enhancer 1.6 Ensembl ENCODE 650.7 +1.7 1735 3.6 PKNOX1 SMAD1 ARNT FEZF1 ZNF2 YY1 POLR2B ZNF766 ZNF213 E2F8 GC0XM073852 XIST ENSG00000278039 RAB11FIP1P1 JPX FTX DDX3P1 RN7SL648P TOMM20P4 ENSG00000271199
GH0XJ073855 Enhancer 0.7 ENCODE 0.7 -3.0 -2968 0.2 CTCF ZNF2 RAD21 RELA ZNF324 CC2D1A ZNF213 ARID2 ZNF143 SMC3 XIST FXYD6P3
GH0XJ073846 Enhancer 0.5 ENCODE 0.4 +5.4 5380 0.9 SP1 NANOG ZNF138 POU5F1 PIR37804 JPX ENSG00000278039 XIST
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for XIST Gene

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

Genomic View for XIST Gene

Genes around XIST on UCSC Golden Path with GeneCards custom track

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

Graphical View of Domain Structure for InterPro Entry

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

No data available for Protein Domains , Suggested Antigen Peptide Sequences 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

Animal Model Products

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 2

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

No Data Available

Interacting Proteins for XIST Gene

Gene Ontology (GO) - Biological Process for XIST Gene


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

Drugs & Compounds for XIST Gene

No Compound Related Data Available

Transcripts for XIST Gene

mRNA/cDNA for XIST Gene

Unigene Clusters for XIST Gene

X inactive specific transcript (non-protein coding):
Representative Sequences:

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

No ASD Table

Relevant External Links for XIST Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for XIST Gene

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

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

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

NURSA nuclear receptor signaling pathways regulating expression of XIST Gene:


SOURCE GeneReport for Unigene cluster for XIST Gene:

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 , Evidence on tissue expression from TISSUES 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

Sequence variations from dbSNP and Humsavar for XIST Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000108401 -- 73,842,683(-) G/A non_coding_transcript_variant
rs1000302728 -- 73,846,331(-) T/C non_coding_transcript_variant
rs1000336578 -- 73,851,209(-) C/T non_coding_transcript_variant
rs1000477310 -- 73,825,179(-) T/C non_coding_transcript_variant
rs1000660967 -- 73,836,138(-) A/C intron_variant

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 , Structural Variations from Database of Genomic Variants (DGV) and Variation tolerance for XIST Gene

Disorders for XIST Gene

MalaCards: The human disease database

(24) MalaCards diseases for XIST Gene - From: LncRNADisease, HGMD, 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
acute lymphocytic leukemia
  • acute lymphoblastic leukemia
- elite association - COSMIC cancer census association via MalaCards
Search XIST in MalaCards View complete list of genes associated with diseases

Additional Disease Information for XIST

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 22 58
  2. 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 22 58
  3. 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 22 58
  4. 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 22 58
  5. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. (PMID: 2034279) Brockdorff N … Rastan S (Nature 1991) 2 3 58

Products for XIST Gene

Sources for XIST Gene

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