Supplementary Figure 2: Cartoon describing the four different splice junction annotation classes, relative to annotated exons.

(A) Annotated splice junctions map between two exons (dark blue rectangles) in a known transcript. (B) Exon-skipping splice junctions map to two annotated exons in different transcripts. (C) Alternative start/exon junctions map to only one annotated exon on either the 5’ or 3’ end. (D) Completely novel junction do not map to any known exon.