Figure 3.

Rules for adding UTRs to genewise predictions: (A) Simplest case: Ends of exons A and D coincide, thus exon A is extended to include the UTR and the translation start is maintained. Starts of exons C and F coincide, thus UTR exons are added and the translation stop is maintained. The coordinates of genewise-derived exon B are used in preference over exon F. (B) cDNA prediction rejected: Neither the ends of exons G and I nor the starts of exons H and J coincide, so the genewise-predicted structure is unmodified. (C) cDNA prediction with short exons: The ends of the exons K and M and the starts of exons L and N coincide. Even though K is shorter than M, it is not the first exon of the cDNA prediction and is thus retained. However, N is shorter than L and there are no additional exons, so it is rejected.