Transcript: TSIX:1

Basic information

LNCipedia transcript ID: TSIX:1 
HGNC Gene Symbol: TSIX    
HGNC Full Gene Name: TSIX transcript, XIST antisense RNA
Ensembl Gene ID: ENSG00000270641
Ensembl Transcript ID: ENST00000604411
RefSeq ID: NR_003255
Location (hg19): chrX:73012040-73049066
Strand: +
Class: intergenic
Sequence Ontology term: lincRNA
Transcript size: 37027 bp
Exons: 1
Sources: NONCODE v4; Ensembl release 75 - Feb 2014; Ensembl release 83 - Dec 2015; Ensembl release 87 - Dec 2016; Ensembl release 90 - Aug 2017; Ensembl release 92 - Apr 2018; Refseq - NCBI Annotation Release 106
Alternative transcript names: NONHSAT137539; NR_003255; ENST00000604411.1; NR_003255.2
Alternative gene names: ENSG00000270641.1; TSIX; NCRNA00013; XIST-AS1; LINC00013


RNA sequence:

Structure:

Protein coding potential

Metric Raw result Interpretation
PRIDE reprocessing 2.0 0 non-coding 
Lee translation initiation sites 0 non-coding 
PhyloCSF score 25.5295 non-coding 
CPAT coding probability 7.17% non-coding 
Bazzini small ORFs 0 non-coding 

In stringent set: yes

Locus conservation

Locus conservation?
TSIX:1 no no no no

Available literature

  1. Wang (2016), Long non-coding RNA TSIX is upregulated in scleroderma dermal fibroblasts and controls collagen mRNA stabilization., Exp. Dermatol.
  2. Peffers (2015), Transcriptome analysis of ageing in uninjured human Achilles tendon., Arthritis Res. Ther.
  3. Quek (2015), lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs., Nucleic Acids Res.
  4. Sun (2015), Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling., Epigenomics
  5. Wu (2015), The converging roles of BRD4 and gene transcription in pluripotency and oncogenesis., RNA Dis
  6. Almlöf (2014), Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes., PLoS ONE
  7. Giorgetti (2014), Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription., Cell
  8. Li (2014), A polymorphism rs12325489C>T in the lincRNA-ENST00000515084 exon was found to modulate breast cancer risk via GWAS-based association analyses., PLoS ONE
  9. Maclary (2014), Differentiation-dependent requirement of Tsix long non-coding RNA in imprinted X-chromosome inactivation., Nat Commun
  10. Payer (2014), Coupling of X-chromosome reactivation with the pluripotent stem cell state., RNA Biol
  11. Takahashi (2014), Extracellular vesicle-mediated transfer of long non-coding RNA ROR modulates chemosensitivity in human hepatocellular cancer., FEBS Open Bio
  12. Bhan (2013), Antisense transcript long noncoding RNA (lncRNA) HOTAIR is transcriptionally induced by estradiol., J. Mol. Biol.
  13. McGraw (2013), Loss of DNMT1o disrupts imprinted X chromosome inactivation and accentuates placental defects in females., PLoS Genet.
  14. Weinberg (2013), Long non-coding RNA targeting and transcriptional de-repression., Nucleic Acid Ther
  15. Wood (2013), Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse., Front Genet
  16. Li (2012), AS1DHRS4, a head-to-head natural antisense transcript, silences the DHRS4 gene cluster in cis and trans., Proc. Natl. Acad. Sci. U.S.A.
  17. Chureau (2011), Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region., Hum. Mol. Genet.
  18. Horvath (2011), Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus., Genome Res.
  19. Navarro (2011), [Epigenetic reprogramming: the importance of X inactivation]., Med Sci (Paris)
  20. Lee (1999), Tsix, a gene antisense to Xist at the X-inactivation centre., Nat. Genet.


LNCipedia transcript ID history

LNCipedia version LNCipedia transcript ID
3.1 lnc-CHIC1-1:2
4.0 TSIX:1
4.1 TSIX:1
5.0 TSIX:1
5.1 TSIX:1
5.2 TSIX:1