Fig. 3

pre-mRNA secondary structure features upstream of 5′ss and at the branch site are associated with splicing and alternative splice site selection. a, b SHAPE reactivity profiles across 5′ss, branch point, and 3′ss for in vivo (a) and deproteinized (b) conditions. Average SHAPE reactivity profiles for spliced (red) versus unspliced (black) events are shown. Significantly higher SHAPE reactivities are observed at the − 1 and − 2 nt positions of 5′ss and the branch site for spliced events rather than unspliced events (marked with asterisks, Mann-Whitney test, P values are shown). c SHAPE reactivity profiles for alternative 5′ss events with the distal 5′ss as the major one. Average SHAPE reactivity profiles of both in vivo (dark blue) and deproteinized (light blue) conditions are shown. Significantly higher SHAPE reactivities only appear at − 1 and − 2 positions upstream of the major distal 5′ss rather than the minor proximal 5′ss (Mann-Whitney test, P value = 1.6e−4 and < 2.2e−16 at − 1 and − 2 positions under in vivo condition; P value = 6.1e−9 and < 2.2e−16 at − 1 and − 2 positions under deproteinized condition). d SHAPE reactivity profiles for alternative 5′ss events with the proximal 5′ss as the major one. The significantly higher SHAPE reactivities of − 1 and − 2 positions only appear upstream of the major proximal 5′ss rather than the minor distal 5′ss (Mann-Whitney test, P value = 3.3e−12 at − 1 position under in vivo condition; no significant difference was detected at − 2 position under in vivo condition; P value = 3.1e−5 and < 2.2e−16 at − 1 and − 2 positions under deproteinized condition). e SHAPE reactivity profiles for alternative 3′ss events with the distal 3′ss as the major one. Average SHAPE reactivity profiles of both in vivo (dark purple) and deproteinized (light purple) conditions across different 3′ss and the corresponding branch points are shown. Significantly higher SHAPE reactivity only appears at the branch site of the major distal 3′ss rather than the minor proximal 3′ss (Mann-Whitney test, P value = 1.2e−3 and 2.8e−4 at branch point under in vivo and deproteinized conditions, respectively). f SHAPE reactivity profiles for alternative 3′ss events with the proximal 3′ss as the major one. The significantly higher SHAPE reactivity only appears at the branch point of the major proximal 3′ss rather than the minor distal 3′ss (Mann-Whitney test, P value = 1.4e−2 and 1.7e−3 at the branch point under in vivo and deproteinized conditions, respectively)