Transcript: SNHG1:14

Basic information

LNCipedia transcript ID: SNHG1:14 ?
HGNC Gene Symbol: SNHG1    ?
HGNC Full Gene Name: small nucleolar RNA host gene 1
Location (hg19): chr11:62619762-62622960
Strand: -
Class: intergenic
Transcript size: 748 bp
Exons: 9
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
Alternative transcript names: ENST00000541615; ENST00000541615.1; SNHG1-020; OTTHUMT00000396025.1; NONHSAT021836; ENST00000541615.5
Alternative gene names: ENSG00000255717; SNHG1; ENSG00000255717.1; OTTHUMG00000167743.1; ENSG00000255717.2; ENSG00000255717.6; UHG; NCRNA00057; LINC00057; lncRNA16


RNA sequence:

Structure:

Protein coding potential


Metric Raw result Interpretation
PRIDE reprocessing 2.0 0 non-coding ?
Lee translation initiation sites 3 coding ?
Highest peak:16
PhyloCSF score -26.3815 non-coding ?
CPAT coding probability 2.86% non-coding ?
Bazzini small ORFs 1 coding ?
seqAAMFSPQELTGEGMGQDPSLCKASVTVMFQVFLMTVCLYLTEQLVAIYH
orfFrame7.613944129
covF1Prop0.111111111
In stringent set: no

Locus conservation

Locus conservation?
SNHG1:14 yes no

Secondary structure information

RNAfold image: download
Randfold minimum free energy: -232.24
Randfold P-value: 0.025

Targetting miRNAs

MirTarget2 predictions:
MicroRNAMirTarget2 score ?
hsa-miR-2964a-5p 67.82
hsa-miR-5580-5p 66.94
hsa-miR-4789-5p 60.02
hsa-miR-4656 57.78
hsa-miR-577 55.14
hsa-miR-4646-3p 50.00

Available literature

  1. Ichigozaki (2016), Serum long non-coding RNA, snoRNA host gene 5 level as a new tumor marker of malignant melanoma., Experimental dermatology
  2. Li (2015), Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets., Frontiers in bioengineering and biotechnology
  3. You (2015), Noncoding RNA small nucleolar RNA host gene 1 promote cell proliferation in nonsmall cell lung cancer., Indian journal of cancer
  4. Zhang (2015), Cancer Specific Long Noncoding RNAs Show Differential Expression Patterns and Competing Endogenous RNA Potential in Hepatocellular Carcinoma., PloS one
  5. Zhi (2015), The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma., PloS one
  6. Cao (2013), Analysis of long non-coding RNA expression profiles in gastric cancer., World journal of gastroenterology
  7. Clark (2012), Genome-wide analysis of long noncoding RNA stability., Genome research
  8. Mizutani (2012), Identification and characterization of novel genotoxic stress-inducible nuclear long noncoding RNAs in mammalian cells., PloS one
  9. Mercer (2010), Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation., BMC neuroscience
  10. Friedel (2009), Conserved principles of mammalian transcriptional regulation revealed by RNA half-life., Nucleic acids research
  11. Tanaka-Fujita (2007), Human and mouse protein-noncoding snoRNA host genes with dissimilar nucleotide sequences show chromosomal synteny., RNA (New York, N.Y.)
  12. Pelczar (1998), The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5'-terminal oligopyrimidine gene family., Molecular and cellular biology
  13. Tycowski (1996), A mammalian gene with introns instead of exons generating stable RNA products., Nature


LNCipedia transcript ID history

LNCipedia version Deprecated transcript ID
3.1 lnc-WDR74-1:10
4.0 SNHG1:14
1.3 lnc-WDR74-1:8