Transcript: lnc-SLC39A11-1:3

Basic information

LNCipedia transcript ID: lnc-SLC39A11-1:3 ?
LNCipedia gene ID: lnc-SLC39A11-1
Location (hg19): chr17:70380443-70588943
Strand: -
Class: intergenic
Transcript size: 1747 bp
Exons: 4
Sources: Biogazelle lncRNA chip; Broad Institute; Ensembl release 64 - Sep 2011; NONCODE v4
Alternative transcript names: ENST00000453722; TCONS_00025252; NONHSAT055685
Alternative gene names: ENSG00000227036; XLOC_012568; linc-ABCA5-3; AC007639.1


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 -30.3744 non-coding ?
CPAT coding probability 18.82% non-coding ?
Bazzini small ORFs 0 non-coding ?
In stringent set: yes

Locus conservation

Locus conservation?
lnc-SLC39A11-1:3 yes no

Secondary structure information

RNAfold image: download
Randfold minimum free energy: -872.52
Randfold P-value: 0.001

Targetting miRNAs

MirTarget2 predictions:
MicroRNAMirTarget2 score ?
hsa-miR-5092 73.82
hsa-miR-1972 66.23
hsa-miR-4755-3p 65.91
hsa-miR-4282 58.80
hsa-miR-1915-3p 58.05
hsa-miR-5001-3p 57.58
hsa-miR-3915 55.40
hsa-miR-4434 55.35
hsa-miR-766-3p 54.11
hsa-miR-551b-5p 53.07
hsa-miR-5703 52.43
hsa-miR-4516 51.63
hsa-miR-15a-3p 51.40
hsa-miR-4286 51.23

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-SLC39A11-2:1
3.1 lnc-SLC39A11-1:3