Summary of the transcriptome analysis using PacBio sequencing. (A) A pipeline of SpliceHunter analysis. (B) Eight AS types are defined and examined in this study. (Upper left) Exon e is strictly contained in intron (sj,sj+1) and both primary RNA sequences contain sites sj and sj+1 if TSS and TES lie beyond the dashed vertical lines. The skipping and inclusion of exon e is a symmetric event with respect to the roles of reference and novel transcript. (Upper right) Exon e retains intron (sj,sj+1). Intron retention and intron in exon are symmetric events with respect to the roles of reference and novel transcripts. (Lower left) sj and sj+1 form an alternative donor/acceptor pair. They are contained in both primary RNA sequences if TSS and TES lie beyond the dashed vertical lines. (Lower right) Exons e1 and e2 are novel in transcripts t1 and t2, respectively. Although e2 lies within the primary RNA sequence of t1, it does not constitute an inclusion even according to Definition 2 as long as the TES of t2 lies to the left of the dashed vertical line.
