Fig. 3

Relationship between AS rate and gene features: expression level, number of introns, or length of coding regions. Introns (n = 65,159) and PCIs (n = 1,383,067) were classified into ten bins of equal sample size, according to gene expression levels in WT cells. The AS rate was computed globally within each bin, as the proportion of AS reads among all reads spanning introns (or PCIs) from that bin. Error bars represent the 95% CI of this proportion. a IR rate. b ASSV rate. c Rate of splicing at potential cryptic introns. d, e same as (a, b), but introns were first classified into three bins, according to the number of introns of the gene in which they are located: genes with 1 intron (n = 5606 introns), genes with 2–3 introns (n = 24,452 introns), genes with > 3 introns (n = 35,101 introns). f Same as (c), but PCIs were first classified into three bins, according to the length of the coding region (CDS) in which they are located: CDS < 750 bp (n = 169,030 PCIs), CDS 750–1400 bp (n = 406,460 PCIs), CDS > 1400 bp (n = 807,577 PCIs). a–c AS rates were measured in normal cells (WT, black line) and in NMD-deficient cells (dashed line). d–f AS rates were measured in NMD-deficient cells. Expression levels (RPKM) are represented in log scale