categorize all internal exons as: constitutive exons; A3Es, A5Es, skipped exons, multiply alternatively spliced exons (for example, exons that exhibited both skipping and alternative 5' splice site usage), and exons that contained retained introns. An internal exon present in at least one transcript was identified as a skipped exon if it was precisely excluded in one or more other transcripts, such that the boundaries of both the 5' and 3' flanking exons were the same in the transcripts that included and skipped the exon (for example, exon E3 in Figure 1). Similarly, an internal exon present in at least one transcript was identified as an A3E or A5E if at least one other transcript contained an exon differing in length by the use of an alternative 3' splice site or 5' splice site. The 'core' of an A3E or A5E is defined as the exon portion that is common to all transcripts used to infer the AS event. The extension of an alternatively spliced exon is the exon portion added to the core region by the use of an alternative 3' splice site or 5' splice site) that is present in some, but not all transcripts used to infer the
