Transcript: SOX2-OT:33

Basic information

LNCipedia transcript ID: SOX2-OT:33 
LNCipedia gene ID: SOX2-OT
Location (hg38): chr3:181610541-181699880
Strand: +
Class: intergenic
Sequence Ontology term: lincRNA
Transcript size: 561 bp
Exons: 3
Sources: Biogazelle lncRNA chip; Ensembl release 64 - Sep 2011; Gencode v13; Ensembl release 68 - Jul 2012; NONCODE v4; Ensembl release 75 - Feb 2014; Ensembl release 83 - Dec 2015; Ensembl release 87 - Dec 2016; Ensembl release 90 - Aug 2017
Alternative transcript names: ENST00000485035; ENST00000485035.1; SOX2-OT-013; OTTHUMT00000350431.1; NONHSAT093497
Alternative gene names: ENSG00000242808; RP11-4B14.2; ENSG00000242808.1; SOX2-OT; OTTHUMG00000158186.2; ENSG00000242808.3; ENSG00000242808.7; DKFZp761J1324; NCRNA00043


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 -32.0983 non-coding 
CPAT coding probability 3.65% non-coding 
Bazzini small ORFs 0 non-coding 

In stringent set: yes

Locus conservation

Locus conservation?
SOX2-OT:33 no no no no

Available literature

  1. Iranpour (2016), Expression analysis of four long noncoding RNAs in breast cancer., Tumour Biol.
  2. Shi (2015), Up-regulation of long non-coding RNA Sox2ot promotes hepatocellular carcinoma cell metastasis and correlates with poor prognosis., Int J Clin Exp Pathol
  3. Wang (2015), Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer., Nucleic Acids Res.
  4. Wang (2015), Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer., Sci Rep
  5. Askarian-Amiri (2014), Emerging role of long non-coding RNA SOX2OT in SOX2 regulation in breast cancer., PLoS ONE
  6. Chaudhry (2014), Small nucleolar RNA host genes and long non-coding RNA responses in directly irradiated and bystander cells., Cancer Biother. Radiopharm.
  7. Hou (2014), A long noncoding RNA Sox2ot regulates lung cancer cell proliferation and is a prognostic indicator of poor survival., Int. J. Biochem. Cell Biol.
  8. Shahryari (2014), Two novel splice variants of SOX2OT, SOX2OT-S1, and SOX2OT-S2 are coupregulated with SOX2 and OCT4 in esophageal squamous cell carcinoma., Stem Cells
  9. Zhao (2014), Expression profiles and initial confirmation of long noncoding RNAs in Chinese patients with pulmonary adenocarcinoma., Onco Targets Ther
  10. Chaudhry (2013), Expression pattern of small nucleolar RNA host genes and long non-coding RNA in X-rays-treated lymphoblastoid cells., Int J Mol Sci
  11. Qureshi (2012), Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease., Nat. Rev. Neurosci.
  12. Amaral (2009), Complex architecture and regulated expression of the Sox2ot locus during vertebrate development., RNA
  13. Fantes (2003), Mutations in SOX2 cause anophthalmia., Nat. Genet.


LNCipedia transcript ID history

LNCipedia version LNCipedia transcript ID
1.3 lnc-SOX2-1:14
3.1 lnc-SOX2-1:14
4.0 SOX2-OT:33
4.1 SOX2-OT:33
5.0 SOX2-OT:33
5.1 SOX2-OT:33
5.2 SOX2-OT:33