Figure 4

Scatter plot of the transcript coverage of competitive and tandem donors (A) and acceptors (B). Vertical and horizontal axes refer to the coverage of distal and proximal splice sites; solid and dotted lines mark the transcript means; A5EΔ4 and A3EΔ3 splicing exons are bolded, green and blue mark the ΔP and ΔD (major) splicing exons, respectively. The inset shows the histogram of the log-ratio (R) of the coverage of the distal over the proximal 5'ss (3'ss); curves marked in black show the smoothed distribution (splines, R package). In A) the coverage scatters mainly along the vertical or horizontal axis, which is indicative of preferentially including or excluding the exon extension from the core sequence. The coverage pattern was used to partition all A5Es into two main types, I and II, and a remaining type. The inset shows for the histogram of R a bimodal shape, which is indicative of two subpopulations of A5Es with predominant proximal or distal splice site usage. In B) the overlap between distal and proximal tandem acceptor coverage is comparatively broader, and consequently the histogram of R exhibits a unimodal shape consistent with a single population of A3Es.