Fig. 3

Metrics of sequence and transcript evolution reveal distinct classes of lncRNAs. a Left: Schematic representing alignment signatures found for miRNA host, divergent, snoRNA host, and intergenic lncRNAs. Alignments of identical base pairs transcribed in both species (that is, transcript-transcript identity) is shown in light red while alignments of identical base pairs transcribed only in top species (that is, transcript-genome identity) is shown in light blue. Right: Median transcript-transcript (TTI) (dotted lines) and transcript-genome identity (TGI) (solid lines) from mouse-human alignments of first three exons of miRNA host (orange), divergent (blue), snoRNA host (purple), and intergenic (green) lncRNAs. Each class of lncRNAs displays distinct patterns of TTI. b Boxplots of TGI and TTI, barplot of splice site conservation, and boxplot of insertion/deletion rate (IDR). c Number of lncRNAs in each class in mouse (left), human (middle), and conserved across all studied species (right). Each lncRNA class has individual turnover rates, with miRNA and snoRNA host genes highly conserved in transcription across mammals, and divergent and intergenic lncRNAs evolving much faster