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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

XIST Gene

RNA gene   GIFtS: 33
GCID: GC0XM073040

X Inactive Specific Transcript (Non-Protein Coding)

(Previous names: X (inactive)-specific transcript, X (inactive)-specific...)
(Previous symbol: DXS399E)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 10

Aliases
X Inactive Specific Transcript (Non-Protein Coding)1 2     DXS10892
DXS399E1 2     LINC000012
SXI12 5     NCRNA000012
Long Intergenic Non-Protein Coding RNA 11     swd662
X (Inactive)-Specific Transcript1     XCE5
X (Inactive)-Specific Transcript (Non-Protein Coding)1     XIC5

External Ids:    HGNC: 128101   Entrez Gene: 75032   Ensembl: ENSG000002298077   OMIM: 3146705   
ORGUL members:    fRNAdb10:FR401596      
NCBI13:M97168    
NONCODE14:u4191 n371511 n343048 n371509 n371512 see all 6      
RNAdb15:LIT1596    

Export aliases for XIST gene to outside databases

Previous GC identifers: GC0XU990236 GC0XM071907 GC0XM072823 GC0XM072957 GC0XM066674


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with XIST include x-inactivation, familial skewed, and testicular cancer.

Gene Wiki entry for XIST Gene

fRNAdb sequence ontology for XIST:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_011669.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the XIST gene promoter:
         COUP-TF1   AhR   COUP   CUTL1   HNF-4alpha1   SRY   PPAR-gamma1   COUP-TF   PPAR-gamma2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for XIST

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat XIST


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq13.2   Ensembl cytogenetic band:  Xq13.2   HGNC cytogenetic band: Xq13.2

XIST Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XIST gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM073040:  view genomic region     (about GC identifiers)

Start:
73,040,486 bp from pter      End:
73,072,588 bp from pter
Size:
32,103 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:
     Genatlas biochemistry entry for XIST:
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

Phenotypes:
     12 MGI mutant phenotypes (inferred from 22 alleles(MGI details for Xist):
 behavior/neurological  cellular  embryogenesis  growth/size  hematopoietic system 
 homeostasis/metabolism  immune system  mortality/aging  nervous system  no phenotypic analysis 
 normal  reproductive system 

XIST for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for XIST: Xisttm1.1Nbd Xisttm4.1Nbd Xisttm5Sado Xisttm3Nbd Rps12-ps1/XistRps12-ps1/tm1Nbd Xisttm1Nbd
                                                     Xisttm2.1Nbd Xisttm3.1Nbd Tsix/XistTsix/tm3Sado Xisttm4Sado Xisttm1Jae Rps12-ps1/XistRps12-ps1/tm1.1Nbd Xisttm2.1Jae

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   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for XIST 

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for XIST

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for XIST

Search CenterWatch for drugs/clinical trials and news about XIST

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Clusters for XIST:

X inactive specific transcript (non-protein coding)
Hs.529901  [show with all ESTs], Hs.655450  [show with all ESTs]
Unigene Representative Sequences: AK054860, NR_001564
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000434839(lincRNA) ENST00000421322(lincRNA) ENST00000417942(lincRNA) ENST00000416330(lincRNA) ENST00000429829(lincRNA)(uc004ebm.1)
ENST00000433732(lincRNA) ENST00000602587(lincRNA) ENST00000445814(lincRNA) ENST00000602863(lincRNA) ENST00000602495(lincRNA)

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Inhib. RNA
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat XIST

Additional mRNA sequence: 

AK025198.1 BX648323.1 CR749383.1 NR_001564.2 X56198.1 

24/40 DOTS entries (see all 40):

DT.87046990  DT.216353  DT.95177946  DT.92454322  DT.92454340  DT.95180696  DT.121298593  DT.121298569 
DT.100881877  DT.95164845  DT.121298588  DT.100881876  DT.100881879  DT.100881872  DT.121298575  DT.121298631 
DT.92454325  DT.121298620  DT.439804  DT.91676208  DT.95069057  DT.95180682  DT.95180711  DT.95334976 

24/764 AceView cDNA sequences (see all 764):

BX648323 BM677478 AA987230 AA626197 CB164809 AI611201 AI186932 BQ778166 
AA693541 AI061126 BX473433 BQ638842 AV649491 AI860794 AL603126 AA345570 
AA463487 AI298739 AL701091 CR596835 AI220713 AA342579 CA866869 AA282959 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for XIST:RNAdb

XIST expression in normal human tissues (normalized intensities)      XIST embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGTGACCACC
XIST Expression
About this image


XIST expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/15 selected tissues (see all 15) fully expand
 
 Ovary (Reproductive System)    fully expand to see all 3 entries
         Pre-Granulosa Cells Primordial Follicle
 
 Neural Crest (Gastrulation Derivatives)    fully expand to see all 3 entries
         PureStem SK11, NCr-fac & Meso-prx Progenitor
 
 Eye (Sensory Organs)    fully expand to see all 3 entries
         Glycinergic Amacrine Cells Inner Nuclear Layer
 
 Epidermis (Integumentary System)
         Detroit 551
 
 Ectoderm (Gastrulation Derivatives)
         PureStem ES-210, Ecto-ntu Progenitor

Genevestigator expression for XIST

SOURCE GeneReport for Unigene clusters: Hs.529901 Hs.655450
    SABiosciences Custom PCR Arrays for XIST
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XIST

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of human and mouse.

Orthologs for XIST gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Xist5 inactive X specific transcripts   --   X (46.15 cM) 103460375 


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/586 SNPs in XIST are shown (see all 586)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1820793831,2
--73048136(+) GCAACA/TGATGC 1 -- ds50010--------
rs1870740121,2
--73048230(+) CTCCCA/GCCTGT 1 -- ds50010--------
rs48928041,2
C--73048289(+) gagttC/G/Tgtgac 1 -- ds50010--------
rs1496814881,2
--73048551(+) ACTTAC/TGGTAA 1 -- ds50010--------
rs1915657991,2
C--73048621(+) ACAGTA/GTATTT 1 -- nc-transcript-variant0--------
rs1835599051,2
--73048763(+) ATTCTA/GCATTT 1 -- nc-transcript-variant0--------
rs1454614881,2
C--73048905(+) ACTTCA/GTTTAT 1 -- nc-transcript-variant0--------
rs1483947221,2
C--73049028(+) TCCAAC/TAATCC 1 -- nc-transcript-variant0--------
rs1886013071,2
--73049108(+) ATTAAC/TATTTC 1 -- nc-transcript-variant0--------
rs2009491731,2
--73049177(+) TTATC-/TTCAAC 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for XIST (73040486 - 73072588 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for XIST: --

Human Gene Mutation Database (HGMD): XIST
SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing XIST
DNA2.0 Custom Variant and Variant Library Synthesis for XIST

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 314670OMIM information: 300181    
OMIM disorders: 300087  
7 diseases for XIST:    About MalaCards
x-inactivation, familial skewed    testicular cancer    klinefelter's syndrome    germ cell tumors
prostate cancer    prostatitis    breast cancer


XIST for disorders           About GeneDecksing

1 Novoseek inferred disease relationship for XIST gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
testicular cancer 34.3 1 14723995 (1)


Export disorders for XIST gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for XIST gene, integrated from 9 sources (see all 85):
(articles sorted by number of sources associating them with XIST)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. (PubMed id 1985261)1, 3 Brown C.J....Willard H.F. (1991)
  2. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. (PubMed id 2034279)1, 3 Brockdorff N....Rastan S. (1991)
  3. Inducible XIST-dependent X-chromosome inactivation in human somatic cells is reversible. (PubMed id 17537922)1, 9 Chow J.C....Brown C.J. (2007)
  4. Familial cases of point mutations in the XIST promoter reveal a correlation between CTCF binding and pre-emptive choices of X chromosome inactivation. (PubMed id 15731119)1, 9 Pugacheva E.M....Lobanenkov V.V. (2005)
  5. A promoter mutation in the XIST gene in two unrelated families with skewed X-chromosome inactivation. (PubMed id 9354806)1, 9 Plenge R.M....Willard H.F. (1997)
  6. A revision of the human XIST gene organization and structural comparison with mouse Xist. (PubMed id 10723727)1, 9 Hong Y.K....Strauss W.M. (2000)
  7. Localization of the X inactivation centre on the huma n X chromosome in Xq13. (PubMed id 1985270)1, 9 Brown C.J....Willard H.F. (1991)
  8. Emerging Roles for Long Non-Coding RNAs in Cancer and Neurological Disorders. (PubMed id 22375145)1 Niland C.N....Khalil A.M. (2012)
  9. Mechanisms of long range silencing by imprinted macro non-coding RNAs. (PubMed id 22386265)1 Pauler F.M....Hudson Q.J. (2012)
  10. Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. (PubMed id 21765457)1 Wutz A. (2011)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Disorders
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 7503 HGNC: 12810 AceView: XIST Ensembl:ENSG00000229807 euGenes: HUgn7503
ECgene: XIST H-InvDB: XIST

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for XIST Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for XIST gene:
Search GeneIP for patents involving XIST

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 Search for Antibodies for XIST at Abcam
 See all of Abcam's Antibodies, Kits and Proteins for XIST
 Custom Antibody / Protein Production Service
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 Advantages of Rabbit Monoclonal antibodies
 Abcam protocols and scientific support
 Browse ProSpec Recombinant Proteins




 Browse Proteins at Cloud-Clone Corp.
 Browse Antibodies at Cloud-Clone Corp.
 Browse ELISAs at Cloud-Clone Corp.
 Browse CLIAs at Cloud-Clone Corp.
 Search LifeMap BioReagents cell lines for XIST
 Gene Synthesis
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 Variant Library Synthesis
 Codon Optimization
 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XIST
 Browse SwitchGear 3'UTR luciferase reporter plasmids for XIST
 Browse SwitchGear Promoter luciferase reporter plasmids for XIST
 Search ThermoFisher Antibodies for XIST
 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat XIST
 inGenious Targeting Laboratory - Custom generated mouse model solutions for XIST
 inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for XIST
Customized:
 lentivirus for stable overexpression
 lentivirus expression plasmids for stable overexpression
 adenovirus for overexpression
 Search LSBio for Antibodies for XIST
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
 Time-controlled gene expresssion
       
GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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(GIFtS: 73)
transforming growth factor, beta 1
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