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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

XIST Gene

RNA gene GIFtS: 35
GCID: GC0XM073040

X inactive specific transcript (non-protein coding)

(Previous names: X (inactive)-specific transcript, X (inactive)-specific...)
(Previous symbol: DXS399E)

Explore 10 diseases affiliated with
XIST via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
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		SXI1² ⁵
DXS1089¹ ²		X (Inactive)-Specific Transcript¹
DXS399E¹ ²		X (Inactive)-Specific Transcript (Non-Protein Coding)¹
LINC00001¹ ²		XCE⁵
NCRNA00001¹ ²		XIC⁵
Swd66¹

External Ids:	HGNC: 12810¹	Entrez Gene: 7503²	Ensembl: ENSG00000229807⁷	OMIM: 314670⁵

ORGUL members:	fRNAdb¹⁰:FR401596
	NCBI:M97168
	NONCODE:u4191 n371511 n343048 n371509 n371512	see all 6
	RNAdb: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:

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)

Gene Wiki entry for XIST

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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000023.10 NC_018934.1 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 ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB: --

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

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

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

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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XIST

Animal Models:
     Mouse knock-outs for XIST: Xist^tm1.1Nbd Xist^tm4.1Nbd Xist^tm5Sado Xist^tm3Nbd Rps12-ps1/Xist^{Rps12-ps1/tm1Nbd} Xist^tm1Nbd
                                               Xist^tm2.1Nbd Xist^tm3.1Nbd Tsix/Xist^Tsix/tm3Sado Xist^tm4Sado Xist^tm1Jae Rps12-ps1/Xist^{Rps12-ps1/tm1.1Nbd} Xist^tm2.1Jae
     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

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for XIST

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, 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

8 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000429829(lincRNA)(uc004ebm.1) ENST00000416330(lincRNA) ENST00000421322(lincRNA) ENST00000445814(lincRNA)

ENST00000434839(lincRNA) ENST00000417942(lincRNA) ENST00000433732(lincRNA) ENST00000540864

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Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for XIST Browse OriGene validated miRNA SYBR primer pairs
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Additional cDNA 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):

AW207622 AA626197 AI540603 CA950252 CB216307 AI635459 AA628440 BE644917

BP873609 BX473945 AA342579 AI920884 AW043642 BM504815 AA282959 AL603126

X56197 AI590004 AI363338 AI565133 CB162719 BM724386 BQ638842 CA774532

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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GGTGACCACC

About this image

XIST expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

6 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Kidney

S-shaped Body

Kidney Endothelial Cells

Endothelium

Ovary

Ovigerous Cord

Ovarian Somatic Cells

Ovary

Bone

Bone

Kidney

Kidney

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 7 LifeMap Cells

Name

Category

PureStem™ progenitor T42 (Embryonic Progenitor Cell)

PureStem™ mesenchymal Progenitor SK11 (Embryonic Progenitor Cell)

Adipose, Bone, Cartilage

PureStem™ mesenchymal progenitor SM30 (Embryonic Progenitor Cell)

Adipose, Bone, Cartilage

PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)

Lateral Plate Mesoderm, Neural Crest

PureStem™ progenitor RASMO12 (Embryonic Progenitor Cell)

PureStem™ progenitor T36 (Embryonic Progenitor Cell)

PureStem™ progenitor U31 (Embryonic Progenitor Cell)

Genevestigator expression for XIST

SOURCE GeneReport for Unigene clusters: Hs.529901 Hs.655450

SABiosciences Custom PCR Arrays for XIST

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for XIST Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse / rat 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, UniProtKB, 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

SNP ID	Valid	Clinical significance	Chr X pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs182079383^1,2		--	73040019(+)	`GCAACA/TGATGC`	2	--	ds500¹ nc-transcript-variant		0	--	--	--	--
rs187074012^1,2		--	73040113(+)	`CTCCCA/GCCTGT`	2	--	nc-transcript-variantds500¹		0	--	--	--	--
rs149681488^1,2		--	73040434(+)	`ACTTAC/TGGTAA`	2	--	ds500¹ nc-transcript-variant		0	--	--	--	--
rs191565799^1,2		--	73040504(+)	`ACAGTA/GTATTT`	2	--	nc-transcript-variant		0	--	--	--	--
rs183559905^1,2		--	73040646(+)	`ATTCTA/GCATTT`	2	--	nc-transcript-variant		0	--	--	--	--
rs145461488^1,2	C,	--	73040788(+)	`ACTTCA/GTTTAT`	2	--	nc-transcript-variant		0	--	--	--	--
rs148394722^1,2		--	73040911(+)	`TCCAAC/TAATCC`	2	--	nc-transcript-variant		0	--	--	--	--
rs188601307^1,2		--	73040991(+)	`ATTAAC/TATTTC`	2	--	nc-transcript-variant		0	--	--	--	--
rs200949173^1,2		--	73041060(+)	`TTATC-/TTCAAC`	2	--	nc-transcript-variant		0	--	--	--	--
rs146527891^1,2		--	73041262(+)	`ACTGAG/TTCACT`	2	--	nc-transcript-variant		0	--	--	--	--

HapMap Linkage Disequilibrium report for XIST (73040486 - 73072588 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
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 in human, mouse, rat 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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

XIST for disorders           About GeneDecksing

OMIM gene information: 314670 300181
OMIM disorders: 300087
10 diseases for XIST:    About MalaCards

x inactivation x-inactivation, familial skewed testicular germ cell tumor germ cell tumor

testicular cancer klinefelter's syndrome genetic disease prostate cancer

breast cancer prostatitis

1 Novoseek 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 84):
(articles sorted by number of sources associating them with XIST)

Utopia: connect your pdf to the dynamic
world of online information

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)
Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. (PubMed id 2034279)^{1, 3} Brockdorff N....Rastan S. (1991)
Inducible XIST-dependent X-chromosome inactivation in human somatic cells is reversible. (PubMed id 17537922)^{1, 9} Chow J.C....Brown C.J. (2007)
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)
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)
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)
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)
Emerging Roles for Long Non-Coding RNAs in Cancer and Neurological Disorders. (PubMed id 22375145)¹ Niland C.N....Khalil A.M. (2012)
Mechanisms of long range silencing by imprinted macro non-coding RNAs. (PubMed id 22386265)¹ Pauler F.M....Hudson Q.J. (2012)
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

		AND	OR
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

Name	Description
PharmGKB entry for XIST	Pharmacogenomics, SNPs, Pathways

Intellectual Property for XIST gene
(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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
About This Section


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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes XIST gene at Home site.

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XIST Gene

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XIST Gene

X inactive specific transcript (non-protein coding)

Aliasesfor XIST gene

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Functionfor XIST gene

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for XIST gene

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for XIST gene

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for XIST gene

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for XIST gene

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for XIST gene

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for XIST gene

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for XIST gene

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