Usage of TSSs in eutherian Mbnl3.

For each sample and species, number of reads and percent over the total mapping to each competing splice junction are provided. Competing junctions consist of alternative splice donors (normally resulting from alternative promoters) joint to the same splice acceptor in the third ancestral exon (see scheme in Fig 2A). Each donor annotated in vast-tools is numbered, starting from 0, and the coordinate on the X chromosome is provided in the header (e.g., 3:132413583; donor 3, coordinate chrX:132413583). The coordinates and donor numbers are depicted in S2A–S2C Fig for each species. The color code for each column corresponds to the scheme of Fig 2A: black, canonical long isoform using the first ATG-encoding exon; gray, ancestral TSS skipping the first ATG-encoding exon; red, eutherian-specific TSS; orange, rodent or primate specific TSS. The column “Group” shows the sample groupings using to generate the quantifications displayed in Fig 2C and S2E and S2F Fig. TSS, transcription start site. (XLSX)