Example of a predicted splice graph in A. thaliana. RNA-Seq alignment data were loaded along with gene model annotations to create a composite model that incorporates all available evidence. SpliceGrapher's visualization modules produce color-coded graphs based on the color scheme used by Sircah  that makes it easy to see exons and introns involved in AS events. RNA-Seq read coverage across one of the introns was sufficient to allow SpliceGrapher to identify an intron retention event (exon outlined in blue). In addition, a novel splice junction (highlighted in green) provided SpliceGrapher with evidence for an alternative 3' splicing event (highlighted in orange). The numbers associated with splice junctions indicate the number of reads that align across it. Vertical bands in the background depict exon boundaries in the original gene model.
Rogers et al. Genome Biology 2012 13:R4 doi:10.1186/gb-2012-13-1-r4