Fig. 4

Combined catalog search of lncRNA orthologs recapitulates distinct lncRNA classes. a Existing lncRNA catalogs were combined for large-scale search of lncRNA orthologs between human (left) and mouse (right). Barplot shows number of transcripts contributed from each source. b Mean transcript-transcript (TTI) (solid line) and transcript-genome identity (TGI) (dotted line) across first three exons of miRNA host (orange), divergent (blue), and snoRNA host (purple) genes, recapitulating signatures from smaller search of lncRNA orthologs expressed in pluripotent cells. Error bars represent standard error of the mean. c Boxplots of TGI and TTI, barplot of splice site conservation (SSC), and boxplot of indel rate (IDR) of each lncRNA class. Insertion/deletion rates were not calculated for miRNA host lncRNAs because not enough exonic segments aligned to accurately calculate rate. Two-sample t-test was used to test for significance for all figures, except one-sample t-test was used to test if mean of indel rate is significantly deviated from 0. ** denotes P <0.01 and * denotes P <0.05. d Histograms of TTI (left) and SSC (right) of candidate intergenic lncRNA (lincRNAs) orthologs (solid bars) from combined search as compared to shuffled transcripts (hashed bars). Even among alignments of shuffled transcripts, we found many poorly-aligning orthologs, suggesting they are artifactual from large number of initial transcripts. e Binned scatterplot of TTI and SSC of filtered lincRNA orthologs (TTI >60 % or SSC >0), enriched for true ancestral orthologs. Distribution of filtered TTI is shown on top, along x-axis. Overlaid on scatterplot are data points for lncRNA orthologs found in analysis of pluripotent cells