Tsix MGI Mouse Gene Detail - MGI:1336196 - X (inactive)-specific transcript, opposite strand

Symbol

Tsix
Name

X (inactive)-specific transcript, opposite strand

Feature Type

antisense lncRNA gene

BioType Conflict
IDs

MGI:1336196
NCBI Gene: 22097
Alliance

gene page
Transcription Start Sites

4 TSS

Sequence Map

ChrX:102475123-102528563 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome X, 46.13 cM
Mapping Data

5 experiments

SNPs within 2kb

998 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1336196	antisense lncRNA gene	ChrX:102475123-102528563 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0004743	antisense lncRNA gene	ChrX:100075527-100130888 (+)
A/J	MGP_AJ_G0004721	antisense lncRNA gene	ChrX:100013228-100064718 (+)
AKR/J	MGP_AKRJ_G0004704	antisense lncRNA gene	ChrX:103024648-103085294 (+)
BALB/cJ	MGP_BALBcJ_G0004705	antisense lncRNA gene	ChrX:98810779-98862687 (+)
C3H/HeJ	MGP_C3HHeJ_G0004653	antisense lncRNA gene	ChrX:100538684-100593905 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0004855	antisense lncRNA gene	ChrX:103043968-103096471 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0004291	antisense lncRNA gene	ChrX:97655913-97706496 (+)
CAST/EiJ	MGP_CASTEiJ_G0004610	antisense lncRNA gene	ChrX:84813518-84869396 (+)
CBA/J	MGP_CBAJ_G0004647	antisense lncRNA gene	ChrX:106221991-106282286 (+)
DBA/2J	MGP_DBA2J_G0004663	antisense lncRNA gene	ChrX:99256544-99309840 (+)
FVB/NJ	MGP_FVBNJ_G0004681	antisense lncRNA gene	ChrX:98559438-98613886 (+)
LP/J	MGP_LPJ_G0004744	antisense lncRNA gene	ChrX:101092321-101150826 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0004667	antisense lncRNA gene	ChrX:110879655-110937532 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0004855	antisense lncRNA gene	ChrX:99763347-99819939 (+)
PWK/PhJ	MGP_PWKPhJ_G0004561	antisense lncRNA gene	ChrX:82393056-82447144 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0004495	antisense lncRNA gene	ChrX:85511144-85569717 (+)
WSB/EiJ	MGP_WSBEiJ_G0004653	antisense lncRNA gene	ChrX:98488121-98543615 (+)

Human Ortholog

TSIX, TSIX transcript, XIST antisense RNA

Vertebrate Orthologs

1

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

TSIX, TSIX transcript, XIST antisense RNA
Synonyms

LINC00013, NCRNA00013, XIST-AS, XISTAS, XIST-AS1
Links

HGNC:12377

NCBI Gene ID: 9383
Chr Location

Xq13.2; chrX:73792205-73829231 (+) GRCh38

MGI Vertebrate Homology

Tsix stringent orthology
1 human;1 mouse
HCOP

vertebrate homology predictions: TSIX
Gene Tree

Tsix

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Phenotype Summary

25 phenotypes from 5 alleles in 4 genetic backgrounds
16 phenotypes from multigenic genotypes
21 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

11
Gene trapped

3
Targeted

8
Find Mice (IMSR)

57 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Maternal transmission of a null allele in this imprinted gene prevents Xist accumulation disrupting X-inactivation and causing early embryonic lethality.

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All GO Annotations

7
GO References

4

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

761
Tissues

18
cDNA Data

3
Literature Summary

13

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

GEO

Expression Atlas

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All Sequences

26
RefSeq

1

Ensembl

ENSMUSG00000085715 (Evidence)
NCBI Gene

22097

Representative Sequences				Length	Strain/Species	Flank
	genomic	22097	NCBI Gene Model \| MGI Sequence Detail	53441	C57BL/6J	± kb
	transcript	NR_002844	RefSeq \| MGI Sequence Detail	4306	ZRU/MplStud

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All nucleic 11

Genomic 1

cDNA 4

Primer pair 6

Microarray probesets 1

Summaries

All 65

Developmental Gene Expression 13

Gene Ontology 4

Phenotypes 21
Earliest

J:10451 Fingeroth JD, Comparative structure and evolution of murine CR2. The homolog of the human C3d/EBV receptor (CD21). J Immunol. 1990 May 1;144(9):3458-67
Latest

J:324716 Samanta MK, et al., Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. Nat Commun. 2022 May 11;13(1):2602

TSS for Tsix:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr161721	ChrX:102491318-102491341 (+)	16,207 bp
Tssr161722	ChrX:102491348-102491364 (+)	16,233 bp
Tssr161723	ChrX:102491391-102491402 (+)	16,274 bp
Tssr161724	ChrX:102526304-102526308 (+)	51,183 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 12/10/2024 MGI 6.24