Transcript: lnc-IRX3-80:59

Basic information

LNCipedia transcript ID: lnc-IRX3-80:59 
LNCipedia gene ID: lnc-IRX3-80
Location (hg38): chr16:54889539-54893483
Strand: -
Class: intergenic
Sequence Ontology term: lincRNA
Transcript size: 2340 bp
Exons: 2
Sources: Broad Institute; NONCODE v4
Alternative transcript names: TCONS_00024661; NONHSAT142607
Alternative gene names: XLOC_011949; linc-IRX3-1; LOC643911; LINC00180; CRNDEP


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 -10.6178 non-coding 
CPAT coding probability 0.03% non-coding 
Bazzini small ORFs 0 non-coding 

In stringent set: yes

Locus conservation

Locus conservation?
lnc-IRX3-80:59 yes no no no

Available literature

  1. Xie (2016), Long non-coding RNAs in colorectal cancer., Oncotarget
  2. Cabanski (2015), Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function., RNA Biol
  3. Chen (2015), Differential lncRNA expression profiles in recurrent gliomas compared with primary gliomas identified by microarray analysis., Int J Clin Exp Med
  4. Maguire (2015), SF3B1 mutations constitute a novel therapeutic target in breast cancer., J. Pathol.
  5. Pastori (2015), The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation., Proc. Natl. Acad. Sci. U.S.A.
  6. Ragusa (2015), Non-coding landscapes of colorectal cancer., World J. Gastroenterol.
  7. Szafron (2015), The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues., PLoS ONE
  8. Wang (2015), CRNDE, a long-noncoding RNA, promotes glioma cell growth and invasion through mTOR signaling., Cancer Lett.
  9. Zheng (2015), CRNDE affects the malignant biological characteristics of human glioma stem cells by negatively regulating miR-186., Oncotarget
  10. Barnhill (2014), High expression of CAI2, a 9p21-embedded long noncoding RNA, contributes to advanced-stage neuroblastoma., Cancer Res.
  11. Chi (2014), Role of BC040587 as a predictor of poor outcome in breast cancer., Cancer Cell Int.
  12. Guo (2014), BRAF-activated long non-coding RNA contributes to colorectal cancer migration by inducing epithelial-mesenchymal transition., Oncol Lett
  13. Roberts (2014), The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease., Philos. Trans. R. Soc. Lond., B, Biol. Sci.
  14. Furney (2013), SF3B1 mutations are associated with alternative splicing in uveal melanoma., Cancer Discov
  15. Graham (2011), Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas., Genes Cancer
  16. Lin (2011), RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders., PLoS ONE


LNCipedia transcript ID history

LNCipedia version LNCipedia transcript ID
1.3 lnc-IRX3-3:1
3.1 lnc-IRX3-3:1
4.0 CRNDE:39
4.1 CRNDE:39
5.0 CRNDE:39
5.1 lnc-CFAP20-80:59
5.2 lnc-IRX3-80:59