Figure 2. Splicing complexity across the gene body.

a, Alternative first exons occur in two main configurations: multiple transcription start sites (TSS, pink) and multiple donor sites (DS, light blue). A subset of the genes in the multiple TSS category produce transcripts with different TSSs and shared DSs (red), and a subset of the genes in the DS category produce transcripts with a shared TSS and different DSs (blue). Some genes in the multiple TSS category directly affect the encoded protein (maroon), and similarly for DS (dark blue). Overlap of configurations is radially proportional (units indicate percentage of all spliced genes). b, Poly(A)+ testes (blue) and CNS (orange) stranded RNA-seq of Gβ13F showing complex processing and splicing of the 5'UTR. An expansion of the 5'UTR showing some of the complexity. Transcription of the gene initiates from one of three different promoters (green arrows) terminates at one of ten possible polyA+ addition sites (from adult head poly(A)+seq, red) and generates 235 transcripts. The first exon has two alternative splice acceptors that splice to one of eleven different donor sites. Only five donor sites are shown due to the proximity of splice sites. Four splice donors are represented by the single red line differing by 12, 5 and 19bp respectively. Three splice donors are represented by the single green line differing by 12 and 11bp. Two splice donors are represented by the single purple line differing by 7bp. These splice variants are combined with four proximal internal splices (Supplementary Fig. 3a) to generate the full complement of transcripts. c, Intron retention rates (ψ) across the gene body. The genome-wide mean lengths of exons and introns are connected by red parabolic arcs, which illustrate the upper and lower quartiles of intron retention (across all samples) for introns retained at or above 20 ψ in at least one sample.