Transcript: lnc-SLC39A11-1:1

Basic information

LNCipedia transcript ID: lnc-SLC39A11-1:1 ?
LNCipedia gene ID: lnc-SLC39A11-1
Location (hg19): chr17:70594180-70636611
Strand: -
Class: intergenic
Transcript size: 2265 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; Refseq - Dec 2014; Ensembl release 83 - Dec 2015
Alternative transcript names: ENST00000499674; ENST00000581549.1; LINC00511-018; OTTHUMT00000441438.1; NONHSAT055705; NR_033876
Alternative gene names: ENSG00000245411; AC080037.2; ENSG00000227036.2; LINC00511; OTTHUMG00000132227.4; ENSG00000227036.6


RNA sequence:

Structure:

Protein coding potential


Metric Raw result Interpretation
PRIDE reprocessing 2.0 0 non-coding ?
Lee translation initiation sites 0 non-coding ?
Highest peak:0
PhyloCSF score -32.1568 non-coding ?
CPAT coding probability 8.72% non-coding ?
Bazzini small ORFs 0 non-coding ?
In stringent set: yes

Locus conservation

Locus conservation?
lnc-SLC39A11-1:1 yes no

Secondary structure information

RNAfold image: download
Randfold minimum free energy: -777.48
Randfold P-value: 0.001

Targetting miRNAs

MirTarget2 predictions:
MicroRNAMirTarget2 score ?
hsa-miR-518d-5p 78.19
hsa-miR-518e-5p 78.19
hsa-miR-518f-5p 78.19
hsa-miR-519a-5p 78.19
hsa-miR-519b-5p 78.19
hsa-miR-519c-5p 78.19
hsa-miR-520c-5p 78.19
hsa-miR-522-5p 78.19
hsa-miR-523-5p 78.19
hsa-miR-526a 78.19
hsa-miR-514a-3p 71.56
hsa-miR-4696 70.08
hsa-miR-514b-3p 69.15
hsa-miR-4735-5p 66.86
hsa-miR-590-3p 65.76
hsa-miR-4739 63.53
hsa-miR-3921 63.31
hsa-miR-3681-5p 62.89
hsa-miR-450b-5p 62.56
hsa-miR-548l 61.70
hsa-miR-1226-3p 60.92
hsa-miR-3130-3p 60.04
hsa-miR-3614-5p 59.71
hsa-miR-451b 59.06
hsa-miR-10b-3p 58.86
hsa-miR-4303 58.03
hsa-miR-337-3p 57.90
hsa-miR-4775 56.98
hsa-miR-4653-5p 56.89
hsa-miR-4668-3p 55.96
hsa-miR-1227 55.73
hsa-miR-551b-5p 54.50
hsa-miR-5193 52.33
hsa-miR-3652 51.91
hsa-miR-129-2-3p 51.42
hsa-miR-331-3p 51.28
hsa-miR-129-1-3p 50.62
hsa-miR-4328 50.00

Available literature

  1. Schmidt (2016), The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region., Cell reports


LNCipedia transcript ID history

LNCipedia version Deprecated transcript ID
1.3 lnc-SLC39A11-1:1
3.1 lnc-SLC39A11-1:1