Recognizing alternative splicing events and EST support. The diagram presents the genomic alignments for two alternative gene models (shaded purple) alongside alignments for six ESTs. The models propose two AS events, one in which two introns with different boundaries overlap and another in which one model retains an intron that is absent in the other. For each AS event, an exon in one gene model (called eoverlap) overlaps an intron (labeled ioverlap ) in another gene model; this overlap forms the basis of the AS event detection algorithm described in the Methods section. For the five-prime AS event, which involves an alternative acceptor site, the differentially-spliced intron in Model 1 also overlaps an alternative intron (labeled ialt ) in Model 2. The orange regions represent Difference Regions (DR), segments of genomic sequence that are included in one gene model and not the other. Also shown are ESTs supporting different splicing decisions. For individual AS Events, the gene model that contains the DR is called GP (Gene Present) and the model that lacks the DR is called GA (for Gene Absent); ESTs that overlap a DR can support either the GA or GP choice, but not both. In the case of AS events involving retained introns, overlapping ESTs provide support for removal of the intron when their boundaries coincide with the intron's boundaries. Alternatively, they provide support for retention of the intron when they contain a block of alignment that begins 20 bases on either side of the intron boundary and extends at least 20 bases within it.