Transcript: SNHG5:13

Basic information

LNCipedia transcript ID: SNHG5:13 
LNCipedia gene ID: SNHG5
Location (hg19): chr6:86386725-86388420
Strand: -
Class: intergenic
Sequence Ontology term: lincRNA
Transcript size: 981 bp
Exons: 5
Sources: Biogazelle lncRNA chip; Ensembl release 64 - Sep 2011; Gencode v13; Ensembl release 68 - Jul 2012; NONCODE v4; Ensembl release 75 - Feb 2014
Alternative transcript names: ENST00000369605; ENST00000369605.4; SNHG5-001; OTTHUMT00000041401.2; NONHSAT113855
Alternative gene names: ENSG00000203875; SNHG5; ENSG00000203875.4; OTTHUMG00000015144.2; ENSG00000203875.6; MGC16362; bA33E24.2; U50HG; NCRNA00044; LINC00044


RNA sequence:

Structure:

Protein coding potential

Metric Raw result Interpretation
PRIDE reprocessing 2.0 0 non-coding 
Lee translation initiation sites 2 non-coding 
PhyloCSF score -194.7806 non-coding 
CPAT coding probability 2.20% non-coding 
Bazzini small ORFs 1 coding 
covF1Prop0.193548387
orfFrame8.465242232
seqAAMKGKGFVWKNALECDISARMLKYRFPAGTMALSSVAQWSSSEDAKIHEKTSRTSGRIFNGKSLG

In stringent set: no

Locus conservation

Locus conservation?
SNHG5:13 no no no no

Available literature

  1. Damas (2016), SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization., Nat Commun
  2. Ichigozaki (2016), Serum long non-coding RNA, snoRNA host gene 5 level as a new tumor marker of malignant melanoma., Exp. Dermatol.
  3. Fadista (2014), Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism., Proc. Natl. Acad. Sci. U.S.A.
  4. Rajpathak (2014), Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome., PLoS ONE
  5. Clark (2012), Genome-wide analysis of long noncoding RNA stability., Genome Res.
  6. Friedel (2009), Conserved principles of mammalian transcriptional regulation revealed by RNA half-life., Nucleic Acids Res.
  7. Tanaka-Fujita (2007), Human and mouse protein-noncoding snoRNA host genes with dissimilar nucleotide sequences show chromosomal synteny., RNA
  8. Tanaka (2000), Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma., Genes Cells


LNCipedia transcript ID history

LNCipedia version LNCipedia transcript ID
1.3 lnc-SYNCRIP-2:4
3.1 lnc-SYNCRIP-2:4
4.0 SNHG5:13
4.1 SNHG5:13
5.0 SNHG5:13
5.1 SNHG5:13
5.2 SNHG5:13