Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1261/rna.046342.114
Title (Primary) Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
Author Nitsche, A.; Rose, D.; Fasold, M.; Reiche, K.; Stadler, P.F.
Source Titel RNA : a publication of the RNA Society
Year 2015
Department PROTEOM
Volume 21
Issue 5
Page From 801
Page To 812
Language englisch
Keywords long noncoding RNAs; lncRNA; splice sites; multiple sequence alignments, evolution; conservation; evolutionary plasticity
UFZ wide themes RU3;
Abstract Large-scale RNA sequencing has revealed a large number of long mRNA-like transcripts (lncRNAs) that do not code for proteins. The evolutionary history of these lncRNAs has been notoriously hard to study systematically due to their low level of sequence conservation that precludes comprehensive homology-based surveys and makes them nearly impossible to align. An increasing number of special cases, however, has been shown to be at least as old as the vertebrate lineage. Here we use the conservation of splice sites to trace the evolution of lncRNAs. We show that >85% of the human GENCODE lncRNAs were already present at the divergence of placental mammals and many hundreds of these RNAs date back even further. Nevertheless, we observe a fast turnover of intron/exon structures. We conclude that lncRNA genes are evolutionary ancient components of vertebrate genomes that show an unexpected and unprecedented evolutionary plasticity. We offer a public web service ( that allows to retrieve sets of orthologous splice sites and to produce overview maps of evolutionarily conserved splice sites for visualization and further analysis. An electronic supplement containing the ncRNA data sets used in this study is available at
Persistent UFZ Identifier
Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P.F. (2015):
Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
RNA 21 (5), 801 - 812 10.1261/rna.046342.114