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XIST Gene

RNA gene   GIFtS: 38

GC0XM066674
X (inactive)-specific transcript (non-protein coding)
(Previous name: X (inactive)-specific transcript )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: DXS399E)
Products    

Aliases &
Descriptions
for XIST gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section
Aliases & Descriptions
X (inactive)-specific transcript (non-protein coding)1 2     XCE2 5
DXS10891 2     SXI12 5
swd661 2     X (inactive)-specific transcript1
NCRNA000011 2     DKFZp779P01292
XIC2 5     DXS399E2

External Ids:    HGNC: 128101   Entrez Gene: 75032   Ensembl: ENSG000002298077   

Export aliases for XIST gene to outside databases

Previous GC identifers: GC0XU990236 GC0XM071907 GC0XM072823 GC0XM072957


Summaries
for XIST gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for XIST:
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 XIST gene is expressed
exclusively from the XIC of the inactive X chromosome. The transcript is spliced but apparently does not encode a
protein. The transcript remains in the nucleus where it coats the inactive X chromosome. 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)

Gene Wiki entry for XIST

Genomic Views
for XIST gene

(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the XIST gene promoter:
         PPAR-gamma1   PPAR-gamma2   SRY   YY1   SREBP-1a   SREBP-1c   SREBP-1b   GATA-1   HSF1 (long)   Sox9   
         Other transcription factors

   Search SABiosciences Chromatin IP Primers for XIST

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 


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 gene densities for chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM066674:  view genomic region     (about GC identifiers)

Start:
 66,674,720 bp from pter
End:
 66,706,299 bp from pter
Size:
 31,580 bases
Orientation:
 minus strand

1 alternative location:
ChrX- 73,040,486-73,072,588     
RefSeq DNA sequence:
NC_000023.10  NT_011669.17  

Proteins
for XIST gene

(According to 1UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

Human Recombinant Proteins 
Browse Purified and Recombinant Proteins at Millipore
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Browse recombinant and purified proteins available from Enzo Life Sciences
Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
Browse OriGene Protein Over-expression Lysates
GenScript Purified and Recombinant Proteins for XIST 
Browse Sino Biological Recombinant Proteins
Browse ProSpec Recombinant Proteins

Antibodies for XIST: 
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GenScript Superior Antibodies for XIST 
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Assays for XIST: 
Browse Kits and Assays available from Millipore
Browse ELISAs at Sigma-Aldrich
OriGene Custom Immunoassay Development 
Browse OriGene Fluorogenic Cell Assay Kits 
Browse R&D Systems for biochemical assays
GenScript Custom Assay Services for XIST 
Browse Enzo Life Sciences for kits & assays
Browse ELISAs and CLIAs at Uscn 

Protein Domains/
Families
for XIST gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
   --

Gene Function
for XIST gene

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section
Inhib.
RNA:    		Browse for Gene Knock-down Tools from Millipore
Browse Nano Scale siRNA at Sigma-Aldrich
Sigma-Aldrich siRNA for XIST
Browse shRNA at Sigma-Aldrich
OriGene 29mer shRNA kits in GFP-retroviral vector: XIST
OriGene shRNA RFP: XIST
OriGene basic RS shRNA: XIST
OriGene siRNA: XIST
QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of XIST 
miRNA:Browse microRNA Mimics at Sigma-Aldrich
Browse microRNA target validation systems at Sigma-Aldrich 
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of XIST 
Search SABiosciences for Assays for microRNAs that regulate XIST

Gene
Editing:		Browse CompoZr Knockout ZFN at Sigma-Aldrich 

Clones:Browse Clones for the Expression of Recombinant Proteins Available from Millipore
Browse iPSC Reprogramming Factors at Sigma-Aldrich
OriGene GFP tagged cDNA clones in CMV expression vector: XIST
OriGene Myc/DDK tagged cDNA clones in CMV expression vector: XIST
OriGene untagged cDNA clones in CMV expression vector: XIST
Browse 3'-UTR reporter clones for miRNA target validation 
Browse MicroRNA Expression Plasmids 
GenScript Custom cDNA clone Services for XIST 
Browse Sino Biological Human cDNA Clones

Cell
Lines:  		GenScript Custom overexpressing Cell Line Services for XIST 

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
Animal Models: 13 MGI mutant phenotypes (inferred from 20 alleles) (MGI details for Xist):
behavior/neurologicalcellularembryogenesisgrowth/sizehematopoietic system
immune systemlethality-postnatallethality-prenatal/perinatallife span-post-weaning/agingno phenotypic analysis
normalotherreproductive system

XIST for phenotypes           About GeneDecksing


Pathways & Interactions
for XIST gene

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section

    SABiosciences Custom Pathway-Focused PCR Arrays for XIST 

    SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for XIST

Drugs & Compounds
for XIST gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section
Browse Small Molecules at Sigma-Aldrich
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for XIST


Transcripts
for XIST gene

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section
Inhib.
RNA:     		Browse for Gene Knock-down Tools from Millipore
Browse Nano Scale siRNA at Sigma-Aldrich
Sigma-Aldrich siRNA for XIST
Browse shRNA at Sigma-Aldrich
OriGene 29mer shRNA kits in GFP-retroviral vector: XIST
OriGene shRNA RFP: XIST
OriGene basic RS shRNA: XIST
OriGene siRNA: XIST
QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of XIST 
miRNA: Browse microRNA Mimics at Sigma-Aldrich
Browse microRNA target validation systems at Sigma-Aldrich 
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of XIST 
Search SABiosciences for Assays for microRNAs that regulate XIST
Clones: Browse FLAG tag genes at Sigma-Aldrich
OriGene GFP tagged cDNA clones in CMV expression vector: XIST
OriGene Myc/DDK tagged cDNA clones in CMV expression vector: XIST
OriGene untagged cDNA clones in CMV expression vector: XIST
Browse 3'-UTR reporter clones for miRNA target validation 
Browse OriGene MicroRNA Expression Plasmids 
GenScript Custom cDNA clone Services for XIST 
Primers: OriGene genome-wide validated SYBR primer pairs: XIST
Browse OriGene validated miRNA SYBR primer pairs 
SABiosciences RT2 qPCR Primer Assay for XIST: PPH68694A

Additional cDNA sequence: 

AK025198.1 BX648323.1 CR749383.1 

24/36 DOTS entries (see all 36):

DT.87046990  DT.216353  DT.95177946  DT.92454322  DT.95180696  DT.92454340  DT.121298569  DT.100881877 
DT.95164845  DT.121298588  DT.100881879  DT.121298631  DT.92454325  DT.100881872  DT.121298620  DT.439804 
DT.91676208  DT.95069057  DT.95180682  DT.95180711  DT.95334976  DT.121298593  DT.121298603  DT.121298626 

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

BM504815 AI611201 AV652127 AA045713 AA513019 AA318541 BF116053 AI540603 
AV652192 BF434180 AW513771 AA339496 AI370972 AA600347 H75966 AI635262 
H80721 AI378822 BM992977 AI858403 BU739080 AL701091 BQ632124 CB216307 

1 RNAdb entry of non coding RNAs:

LIT1596   

highest scoring ESTs for XIST:

AA167449 AI811194 AL698978 AL709459 AL710417 AV690829 AV690862 AV693056 AV693074 AW361207 

Unigene Clusters for XIST:

X (inactive)-specific transcript (non-protein coding)
Hs.529901  [show with all ESTs], Hs.727490  [show with all ESTs]
Unigene Representative Sequences: AK054860, BX648323


GeneLoc Exon Structure

7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000434839 ENST00000429829(uc004ebm.1) ENST00000421322 ENST00000433732
ENST00000417942 ENST00000445814 ENST00000416330

Expression
for XIST gene

(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

XIST expression in normal and diseased human tissues

1  / 2  / 3

19 probe-sets matching XIST gene

Affymetrix
probe-set		 Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
45324_at2, 3 U95-B 1 0.88 1.00 0.93 1.48 AA167449 0.80 1.00 0.91 1
83984_at2, 3 U95-E 1 0.81 1.00 0.95 1.42 AL037999 0.40 1.00 0.76 1
64429_at2, 3 U95-C 1 0.81 1.00 0.53 0.76 AA214086 0.60 1.00 0.82 1
55192_at2, 3 U95-B 1 0.75 1.00 -0.34 0.80 W32551 0.60 1.00 0.82 1
38446_at2, 3 U95-A 1 0.62 1.00 0.84 0.64 X56199 0.60 1.00 0.82 1
243712_at2, 3 U133-B 1 0.91 1.00 -- -- AA022679 0.40 1.00 0.76 1
214218_s_at2, 3 U133-A 1 0.82 1.00 -- -- AV699347 0.40 1.00 0.76 1
221728_x_at2, 3 U133-A 1 0.73 1.00 -- -- AA628440 0.60 1.00 0.82 1
224588_at2, 3 U133-B 1 0.73 1.00 -- -- AA167449 0.80 1.00 0.91 1
227671_at2, 3 U133-B 1 0.64 1.00 -- -- AV646597 0.40 1.00 0.76 1
224589_at2, 3 U133-B 1 0.64 1.00 -- -- BF223193 0.60 1.00 0.82 1
224590_at2, 3 U133-B 1 0.55 1.00 -- -- BE644917 0.60 1.00 0.82 1
243712_at2 U133Plus2 1 0.91 1.00 -- -- -- -- -- -- --
214218_s_at2 U133Plus2 1 0.82 1.00 -- -- -- -- -- -- --
221728_x_at2 U133Plus2 1 0.73 1.00 -- -- -- -- -- -- --
224588_at2 U133Plus2 1 0.73 1.00 -- -- -- -- -- -- --
227671_at2 U133Plus2 1 0.64 1.00 -- -- -- -- -- -- --
224589_at2 U133Plus2 1 0.64 1.00 -- -- -- -- -- -- --
224590_at2 U133Plus2 1 0.55 1.00 -- -- -- -- -- -- --
About this table

XIST for expression           About GeneDecksing

Data from Genenote  (Publications) and GNF BioGPS
    About these images
XIST gene expression
XIST gene electronic northern expression
XIST gene sage expression
About these images

CGAP SAGE TAG: GGTGACCACC

SOURCE GeneReport for Unigene clusters: Hs.529901 Hs.727490

Expression variation in blood from EXPOLDB for XIST

Primers: OriGene genome-wide validated SYBR primer pairs: XIST
Browse OriGene validated miRNA SYBR primer pairs 
SABiosciences RT2 qPCR Primer Assay for XIST: PPH68694A
    SABiosciences Custom PCR Arrays for XIST 


Orthologs
for XIST gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section
Orthologs for XIST gene from 1 species
Organism Gene Locus Description Human
Similarity		 NCBI accessions
mouse
(Mus musculus)		 Xist5 X (46.15 cM) inactive X specific transcripts   -- X99946 
About this table        Species with no ortholog for XIST

ENSEMBL Gene Tree for XIST (if available)

Paralogs
for XIST gene

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

Genomic Variants
for XIST gene

(SNPs according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
Search QIAGEN SeqTarget long-range PCR primers for resequencing for XIST 

Disorders & Mutations
for XIST gene

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section
XIST for disorders           About GeneDecksing

OMIM: 314670   disorders: 300087  

1 Novoseek disease relationship for XIST gene

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

Human Gene Mutation Database (HGMD): XIST

Export disorders and mutations for XIST gene to outside databases

Medical News
for XIST gene

(Possibly Related Articles in Doctor's Guide)
About This Section
   --

Publications
for XIST gene

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

10/72 PubMed articles for XIST gene, integrated from 7 sources (see all 72):
(articles sorted by number of sources associating them with XIST)
  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, 7 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, 7 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, 7 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, 7 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, 7 Brown C.J....Willard H.F. (1991)
  8. Identification of regulatory elements flanking human XIST reveals species differences. (PubMed id 20211024)1 Chang S.C. and Brown C.J. (2010)
  9. Severe XIST hypomethylation clearly distinguishes (SR Y+) 46,XX-maleness from Klinefelter syndrome. (PubMed id 19812237)1 Poplinski A....Gromoll J. (2010)
  10. 2-D structure of the A region of Xist RNA and its imp lication for PRC2 association. (PubMed id 20052282)1 Maenner S....Branlant C. (2010)

External Searches for XIST gene

(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)

Genome Databases showing XIST gene

(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

Other Databases showing XIST gene

(According to HUGE)
About This Section
   --

Specialized Databases showing XIST gene

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
   --

Intellectual Property
for XIST gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from XenneX, 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



Products
for XIST gene

(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
About This Section

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services

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 "Your Favorite Gene" Pathways and Molecular Interaction Networks Browse Nano Scale siRNA at Sigma-Aldrich
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 miRNA Expression Plasmids

 		 
 QIAGEN Custom miScript Target Protector blocks miRNA-binding site of XIST
 Search QIAGEN SeqTarget long-range PCR primers for resequencing for XIST
 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays
 QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of XIST
 GenScript Purified and Recombinant Proteins for XIST GenScript Custom cDNA clones with any tag delivered in your preferred vector Services for XIST
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 Regulatory tfbs in XIST promoter
 Search Chromatin IP Primers for XIST
 RT2 qPCR Primer Assay for XIST
 GNC Network for XIST
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 Browse ELISAs and CLIAs at Uscn
       

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