Figure 3.

Alternative splicing underlies only a minor fraction of exons with TDU, while the rest are consistent with alternative transcription start or stop sites. The three panels show data from subset A of the GTEx data. Analogous plots for subsets B and C are shown in Supplementary Figure S17. (A) The heights of the bars show the number of exonic regions with TDU, grouped according to the number of reads that support their splicing out from transcripts. Most exonic regions with TDU have either no or weak evidence of being spliced out from transcripts (bar colored in pink salmon). The bar colors serve also as color legends for Figure 3B and C. (B) Each point represents one of the 47 659 exonic regions that were detected to be used in a tissue-dependent manner. The X-axis shows the fraction of REUC variance that is attributed to variance between tissues (R²). Analogously, the Y-axis shows the R² statistic for the RSICs. Exonic regions with strong evidence of being spliced out from transcripts (purple points) lay along the diagonal. (C) Cumulative distribution functions of the Pearson correlation coefficients between the REUCs and the RSICs are shown for exonic regions with TDU. The regions are stratified according to the number of sequenced fragments supporting their splicing out from transcripts. The REUCs and RISCs are highly correlated for the minor fraction of exons that have strong evidence of being spliced out from transcripts (purple line).