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Symbol XIST contributors: mct - updated : 07-05-2011
HGNC name X (inactive)-specific transcript
HGNC id 12810
Location Xq13.2      Physical location : 73.040.494 - 73.072.588
Synonym name DNA segment, single copy, probe 8A11
Synonym symbol(s) DXS1089, DXS399E, XCE, XIC, SXI1, swd66
TYPE small rna
SPECIAL FEATURE overlapping, gene in gene
  • 3' end overlapped by 3' end of TSIX
  • expressed only on the inactivated X, not the active X
  • STRUCTURE 32.00 kb     6 Exon(s)
    regulatory sequence Promoter
    Binding site
    text structure
  • histone 3 lys 9 methylation hot spot upstream the promoter
  • one homologous CTCF-binding sequence with the matching dG-contacts, which include the -43 position within the DNase I footprint of CTCF
  • MAPPING cloned Y linked N status confirmed
    Map cen - DXS453 - DXS131 - RPS4X - PHKA1 - DXS1164 - DXS227 - DXS1677 - [NAP1L2 - CDX4 - DXS1005E - XIST - RPSAP14 ] - DXS1166 - SLC16A2 - DXS441 - DXS171 - DXS347 - DXS325 - DXS356 - DXS56 - ATP7A (MNK )- PGK1 PGK1 PGK1 PGK1 - qter
    Authors Brown (91), Lafrenière (93), Horn (95), Consensus (95), Rougeulle(96)
    Text [XIC region]
    Physical map
    CXCR3 Xq13 chemokine (C-X-C motif) receptor 3 LOC158825 Xq13.1 hypothetical LOC158825 LOC389868 X LOC389868 LOC389869 X LOC389869 LOC389870 X LOC389870 LOC389871 X LOC389871 LOC286539 Xq13.1 similar to 40S ribosomal protein S26 KIAA2001 Xq13.1 KIAA2001 protein LOC340527 Xq13.1 similar to Nance-Horan syndrome (congenital cataracts and dental anomalies); NHS gene LOC392490 X similar to Translationally controlled tumor protein (TCTP) (p23) (Histamine-releasing factor) (HRF) PIN4 Xq13 protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin) FLJ20105 Xq13.1 hypothetical protein FLJ20105 RPS4X Xq13.1 ribosomal protein S4, X-linked CITED1 Xq13.1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 HDAC8 Xq13 histone deacetylase 8 PHKA1 Xq13.1 phosphorylase kinase, alpha 1 (muscle) DMRTC1 Xq13.1 DMRT-like family C1 MGC34827 Xq13.1 hypothetical protein MGC34827 LOC340529 Xq13.1 hypothetical protein LOC340529 LOC392491 X similar to hypothetical protein LOC340529 LOC392492 X similar to Nap1l2 NAP1L2 Xq13.2 nucleosome assembly protein 1-like 2 LOC392493 X hypothetical gene supported by BC000882; NM_014765 LOC392494 X similar to YWHAZ protein CDX4 Xq13.2 caudal type homeo box transcription factor 4 LOC139201 Xq13.1 mitogen-activated protein kinase kinase 4 pseudogene LOC389872 X similar to cysteine-rich hydrophobic 1 (CHIC1) protein LOC389873 X similar to selenophosphate synthetase 1 XIST Xq13.2 X (inactive)-specific transcript LOC260337 Xq13.1 zinc finger protein Np97 pseudogene LOC139932 Xq13.1 similar to DEAD-box protein 3 (Helicase-like protein 2) (HLP2) (DEAD-box, X isoform) MKRNP1 Xq13 makorin, ring finger protein, pseudogene 1 LOC347359 Xq13.1 similar to BMP-2 inducible protein kinase (BIKe) (HRIHFB2017) LOC392496 X similar to Rab coupling protein; Rab-interacting recycling protein; Rab effector protein; rab11-family interacting protein 1 LOC389874 X cellular nucleic acid binding protein-like LOC392497 X similar to 40S ribosomal protein S6 (Phosphoprotein NP33) LOC286493 Xq13.2 similar to Interferon-inducible, double stranded RNA dependent inhibitor, protein-kinase LOC392498 X similar to 40S ribosomal protein S7 (S8) SLC16A2 Xq13.2 solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter) PABPCP3 Xq13 poly(A) binding protein, cytoplasmic, pseudogene 3 RNF12 Xq13-q21 ring finger protein 12 KIAA2022 Xq13.2 KIAA2022 protein ABCB7 Xq13 ATP-binding cassette, sub-family B (MDR/TAP), member 7 MGC23937 Xq13.2 hypothetical protein MGC23937 similar to CG4798 LOC389875 X similar to telomeric repeat binding factor 1 isoform 2; Telomeric repeat binding factor 1; telomeric repeat binding protein 1 ZDHHC15 Xq13.1 zinc finger, DHHC domain containing 15 BRAF2 Xq13.2 similar to v-raf murine sarcoma viral oncogene homolog B1 pseudogene LOC286495 Xq13.2 similar to Tetratricopeptide repeat protein 3 (TPR repeat protein D) HCA3 Xq13.2 hepatocellular carcinoma-associated protein HCA3
    regionally located in the region of the X inactivation center
    TRANSCRIPTS type untranslated
    text untranslated RNA
    Rna function XIST RNA is diffusible and is trapped by the X chromosome via YY1
       expressed in (based on citations)
    cell lineage
    cell lines
    at STAGE
    CATEGORY regulatory
    SUBCELLULAR LOCALIZATION     intracellular
    text non chromatin nuclear structure
    basic FUNCTION
  • associating with inactive X and involved in chromatin packaging
  • involved in the overexpression of H2A1M in inactivated X
  • implicated in recognizing the number of X chromosomes and initiating a silencing signal on cis
  • delayed reprogramming of XIST/reactivation of inactive X chromosome after cell fusion was accelerated by DNA methylation and histone deacetylation of XIST, which follow upregulation of DNMT3A and TSIX
  • reprogramming of X-chromosome inactivation during the acquisition of pluripotency is accompanied by the repression of XIST, the trigger of X-inactivation, and the upregulation of its antisense counterpart TSIX (
    a component possible constituent of non chromatin nuclear structure
    RNA binding to XIST RNA with the hot spot of H3lys9
    small molecule
  • YY1 interacts with XIST RNA through Repeat C
  • cell & other
    inhibited by trichostatin A, which normally activates gene expression, but results in downregulation of XIST
    repressed by TSIX, its transcription is negatively regulated by its antisense partner TSIX, whose disruption results in nonrandom X-chromosome inactivation in females
    Other replication regulated (replicated before its expressed allele)
    methylation is the initial event in the spread of the inactivation signal
    maintenance of XIST methylation is controlled differently than global genomic methylation and in the absence of both DNMT1 and DNMT3B
    regulated by a balance of multiple XIST activators and repressors, and levels of POU5F1 and TSIX are crucial toward achieving this balance
    corresponding disease(s)
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional germinal mutation      
    promoter mutated in skewed X inactivation and the choice of X chromosome inactivation reflects stabilization of a higher order chromatin conformation impinging on the CTCF-XIST promoter complex
    tumoral     --other  
    aberrantly demethylated in testicular germ cell tumor and in male-derived plasma
    tumoral     --over  
    by demethylation in aggressive prostate cancer
    Variant & Polymorphism
    Candidate gene
    Therapy target