Transcript: lnc-SLC39A11-1:7

Basic information

LNCipedia transcript ID: lnc-SLC39A11-1:7 ?
LNCipedia gene ID: lnc-SLC39A11-1
Location (hg19): chr17:70399469-70588941
Strand: -
Class: intergenic
Transcript size: 1956 bp
Exons: 5
Sources: Biogazelle lncRNA chip; Broad Institute; Ensembl release 64 - Sep 2011; NONCODE v4
Alternative transcript names: ENST00000457958; TCONS_00025253; NONHSAT055689
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 13.2115 non-coding ?
CPAT coding probability 1.70% non-coding ?
Bazzini small ORFs 0 non-coding ?
In stringent set: yes

Locus conservation

Locus conservation?
lnc-SLC39A11-1:7 yes no

Secondary structure information

RNAfold image: download
Randfold minimum free energy: -685.64
Randfold P-value: 0.003

Targetting miRNAs

MirTarget2 predictions:
MicroRNAMirTarget2 score ?
hsa-miR-126-5p 97.09
hsa-miR-4795-3p 93.11
hsa-miR-515-5p 90.12
hsa-miR-519e-5p 89.59
hsa-miR-1253 86.23
hsa-miR-5585-5p 78.19
hsa-miR-5092 73.82
hsa-miR-581 67.38
hsa-miR-192-5p 66.61
hsa-miR-215 66.58
hsa-miR-129-5p 64.30
hsa-miR-4457 63.19
hsa-miR-5196-3p 60.90
hsa-miR-4434 60.31
hsa-miR-1910 59.48
hsa-miR-5681a 59.17
hsa-miR-1303 58.75
hsa-miR-4793-3p 58.45
hsa-miR-5703 58.30
hsa-miR-4516 58.01
hsa-miR-548aw 57.76
hsa-miR-630 57.61
hsa-miR-767-5p 57.27
hsa-miR-4781-3p 55.03
hsa-miR-2355-3p 54.71
hsa-miR-3922-5p 54.70
hsa-miR-4286 53.49
hsa-miR-3936 53.39
hsa-miR-551b-5p 53.07
hsa-miR-3173-5p 52.82
hsa-miR-766-3p 51.70
hsa-miR-193a-3p 51.15

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-SLC39A11-2:4
3.1 lnc-SLC39A11-1:7