Conservation of splicing patterns across species. (A) Conservation of exon boundaries. The distributions show the difference of exon boundaries of reference exons from the human GENCODE annotation and predicted exons in the other species. (B) Normalized read density in a window of 50 nucleotides around splice sites in human and mouse. Both 5′- and 3′-splice sites are shown. Only splice sites for which at least half of the positions could be aligned in mouse were considered. The graph at the bottom right shows the SiPhy conservation scores for splice sites in mouse. The mean score averaged over all aligned positions in the 50-nt window and a running average over 100 splice sites is shown. (C) Averaged normalized read count in a 50-nt window around 3′- and 5′-splice sites in human, rhesus, cow, and mouse. Again, only splice sites with more than half the positions in the window aligned were considered. Also, only “split reads” that map to two regions across an exon/intron boundary were counted. (D) Splice-site conservation patterns of individual transcripts. Each line represents a transcript. Each group of boxes represents a splice site (both 3′- and 5′-sites are shown separately, i.e., two splice sites means a transcript has two exons and one intron). Each box within a group indicates the conservation status in the different species. All multiexon lincRNAs are shown for which we could detect significant expression (P < 0.1; Methods) in human, chimpanzee, rhesus, cow, mouse, and rat. All known lincRNAs from lincRNAdb are included and highlighted with their name. If a locus had multiple isoforms, the isoform with the most confirmed human splice sites is shown, which is not necessarily the most abundant transcript.
