Xist MGI Mouse Gene Detail - MGI:98974 - inactive X specific transcripts

Symbol

Xist
Name

inactive X specific transcripts

Feature Type

lncRNA gene
IDs

MGI:98974
NCBI Gene: 213742
Alliance

gene page
Transcription Start Sites

21 TSS

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

SNPs within 2kb

396 from dbSNP Build 142
Strain Annotations

18
RFLP

5

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_98974	lncRNA gene	ChrX:102503972-102526860 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0007554	lincRNA gene	ChrX:100105215-100129148 (-)
A/J	MGP_AJ_G0007553	lincRNA gene	ChrX:100040721-100062978 (-)
AKR/J	MGP_AKRJ_G0007523	lincRNA gene	ChrX:103058913-103083554 (-)
BALB/cJ	MGP_BALBcJ_G0007527	lincRNA gene	ChrX:98838174-98860947 (-)
C3H/HeJ	MGP_C3HHeJ_G0007474	lincRNA gene	ChrX:100568330-100592165 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0007700	lincRNA gene	ChrX:103072506-103094731 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0006877	lincRNA gene	ChrX:97682958-97704771 (-)
CAST/EiJ	MGP_CASTEiJ_G0007376	lincRNA gene	ChrX:84843440-84867656 (-)
CBA/J	MGP_CBAJ_G0007455	lincRNA gene	ChrX:106258542-106280546 (-)
DBA/2J	MGP_DBA2J_G0007480	lincRNA gene	ChrX:99285277-99308100 (-)
FVB/NJ	MGP_FVBNJ_G0007496	lincRNA gene	ChrX:98589955-98612146 (-)
LP/J	MGP_LPJ_G0007560	lincRNA gene	ChrX:101123703-101149086 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0007476	lincRNA gene	ChrX:110912285-110935792 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0007703	lincRNA gene	ChrX:99796259-99818199 (-)
PWK/PhJ	MGP_PWKPhJ_G0007314	lincRNA gene	ChrX:82421835-82445404 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0007218	lincRNA gene	ChrX:85543143-85567986 (-)
WSB/EiJ	MGP_WSBEiJ_G0007437	lincRNA gene	ChrX:98516010-98541875 (-)

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
Links

HGNC:12810

NCBI Gene ID: 7503
Chr Location

Xq13.2; chrX:73820649-73852753 (-) GRCh38

MGI Vertebrate Homology

Xist stringent orthology
1 human;1 mouse
HCOP

vertebrate homology predictions: XIST
Gene Tree

Xist

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Phenotype Summary

13 phenotypes from 16 alleles in 8 genetic backgrounds
32 phenotypes from multigenic genotypes
64 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

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.

All Mutations and Alleles

28
Endonuclease-mediated

2
Targeted

26
Genomic Mutations

1 involving Xist
Find Mice (IMSR)

8 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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.

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All GO Annotations

11
GO References

10

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

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

1036
Tissues

88
cDNA Data

29
Literature Summary

81

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

47
RefSeq

2

Ensembl

ENSMUSG00000086503 (Evidence)
NCBI Gene

213742

Representative Sequences				Length	Strain/Species	Flank
	genomic	213742	NCBI Gene Model \| MGI Sequence Detail	22861	C57BL/6J	± kb
	transcript	NR_001463	RefSeq \| MGI Sequence Detail	17918	Not Specified

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All nucleic 158

Genomic 94

cDNA 36

Primer pair 18

Other 10

Microarray probesets 6

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MGD-MRK-15474, MGI:2147863

Summaries

All 299

Developmental Gene Expression 81

Gene Ontology 10

Phenotypes 64
Earliest

J:2970 Brown SD, XIST and the mapping of the X chromosome inactivation centre. Bioessays. 1991 Nov;13(11):607-12
Latest

J:346696 Wei C, et al., Imprinted X chromosome inactivation at the gamete-to-embryo transition. Mol Cell. 2024 Feb 29;

TSS for Xist:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr163959	ChrX:102526849-102526858 (-)	-15 bp
Tssr163958	ChrX:102526811-102526831 (-)	18 bp
Tssr163957	ChrX:102526640-102526648 (-)	195 bp
Tssr163956	ChrX:102526438-102526455 (-)	392 bp
Tssr163955	ChrX:102526386-102526400 (-)	446 bp
Tssr163954	ChrX:102526156-102526183 (-)	669 bp
Tssr163953	ChrX:102524489-102524541 (-)	2,324 bp
Tssr163952	ChrX:102524389-102524402 (-)	2,443 bp
Tssr163951	ChrX:102524299-102524375 (-)	2,502 bp
Tssr163950	ChrX:102524169-102524251 (-)	2,629 bp
Tssr163949	ChrX:102524116-102524167 (-)	2,697 bp
Tssr163948	ChrX:102521748-102521753 (-)	5,088 bp
Tssr163947	ChrX:102519259-102519281 (-)	7,569 bp
Tssr163946	ChrX:102519182-102519231 (-)	7,632 bp
Tssr163945	ChrX:102516604-102516608 (-)	10,233 bp
Tssr163942	ChrX:102512519-102512533 (-)	14,313 bp
Tssr163941	ChrX:102511618-102511642 (-)	15,209 bp
Tssr163940	ChrX:102511060-102511160 (-)	15,729 bp
Tssr163939	ChrX:102510895-102510944 (-)	15,919 bp
Tssr5663	ChrX:102510221-102510238 (-)	16,609 bp
Tssr163938	ChrX:102504009-102504035 (-)	22,817 bp

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 Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24