Given an input genomic sequence and the locations of gene regions, our goal is to find the functional exons originating from each gene locus, identifying their respective amino acid codons and splice sites. Figure 1 shows examples of alternatively spliced exons examined in this study: intron retention (IR), cassette exon (CE), and multiple splice sites (MS). Also considered are constitutive exons (CS), defined to be an exon included with the same splice site boundaries in all functional mRNA forms.