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Xist Gene Detail
Summary
  • Symbol
    Xist
  • Name
    inactive X specific transcripts
Location &
Maps
more
  • Sequence Map
    ChrX:102503979-102526839 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome X, 46.15 cM, cytoband D
  • Mapping Data
    62 experiments
Strain
Comparison
more
  • SNPs within 2kb
    396 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    5
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98974
 lncRNA gene ChrX:102503972-102537573 (-)
129S1/SvImJ ENSMUSG00200039043
 lncRNA gene ChrX:84269090-84291962 (-)
A/J ENSMUSG00195040653
 lncRNA gene ChrX:88023808-88046682 (-)
AKR/J ENSMUSG00220038294
 lncRNA gene ChrX:82691462-82714333 (-)
BALB/cJ ENSMUSG00180042161
 lncRNA gene ChrX:84701079-84723953 (-)
C3H/HeJ ENSMUSG00175046280
 lncRNA gene ChrX:88273939-88296811 (-)
C57BL/6NJ ENSMUSG00215046253
 lncRNA gene ChrX:84881002-84903892 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0006877
 lincRNA gene ChrX:97682958-97704771 (-)
CAST/EiJ ENSTCUG00005043238
 lncRNA gene ChrX:85744524-85767432 (-)
CBA/J ENSMUSG00210046507
 lncRNA gene ChrX:85164755-85187628 (-)
DBA/2J ENSMUSG00185045825
 lncRNA gene ChrX:97603957-97626827 (-)
FVB/NJ ENSMUSG00205041811
 lncRNA gene ChrX:84246213-84269087 (-)
JF1/MsJ ENSUMUG00000038015
 lncRNA gene ChrX:118211793-118234758 (-)
LP/J ENSMUSG00230042474
 lncRNA gene ChrX:104302272-104325143 (-)
NOD/ShiLtJ ENSMUSG00190037831
 lncRNA gene ChrX:84322567-84345438 (-)
NZO/HlLtJ ENSMUSG00225045675
 lncRNA gene ChrX:109422590-109445456 (-)
PWK/PhJ ENSLUMG00010037640
 lncRNA gene ChrX:83526410-83549397 (-)
SPRET/EiJ ENSMSPG00010042785
 lncRNA gene ChrX:87730821-87753666 (-)
WSB/EiJ ENSIUOG00005044169
 lncRNA gene ChrX:84826037-84848897 (-)



Homology
more
  • Human Ortholog
    XIST, X inactive specific transcript
  • Vertebrate Orthologs
    1
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    XIST, X inactive specific transcript
  • Synonyms
    DXS1089, DXS399E, LINC00001, NCRNA00001, swd66, SXI1, XIC
  • Links
    NCBI Gene ID: 7503

  • Chr Location
    Xq13.2; chrX:73820649-73852714 (-)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    11 phenotypes from 12 alleles in 6 genetic backgrounds
    34 phenotypes from multigenic genotypes
    77 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Xist function in X-inactivation is disrupted in females carrying a null mutation. Depending on maternal or paternal derivation of the mutation, females survive or die in early embryogenesis. In either case, X-inactivation is non-random and abnormal.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    968
  • Tissues
    94
  • cDNA Data
    31
  • Literature Summary
    85
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    • All Sequences
      49
    • RefSeq
      2
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 213742 NCBI Gene Model | MGI Sequence Detail 22861 C57BL/6J ±  kb
    transcript NR_001463 RefSeq | MGI Sequence Detail 17918 Not Specified  
    For the selected sequence
    Molecular
    Reagents
    less
    • All nucleic 165
      Genomic 94
      cDNA 38
      Primer pair 22
      Other 11

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGD-MRK-15474, MGI:2147863
    References
    more
    • Summaries
      All 322
      Developmental Gene Expression 85
      Phenotypes 77
    • Earliest
      J:2970 Brown SD, XIST and the mapping of the X chromosome inactivation centre. Bioessays. 1991 Nov;13(11):607-12
    • Latest
      J:387477 Lovell CD, et al., Female mice with a Xist deletion in B cells can develop lupus-associated phenotypes. Cell Rep. 2026 Jun 11;45(6):117517
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/15/2026
    MGI 6.29     		The Jackson Laboratory