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Identification of Shadow Exons: Mining for Alternative Exons in Human, Mouse and Rat Comparative Databases

We describe a comparative analysis of alternative exons in mammalian transcriptomes, designed to identify species-specific and conserved alternative splicing events. We mine the comparative alternative splicing databases of human, mouse and rat to identify previously unobserved alternative exons termed here as shadow exons. Using established genome synteny maps together with sequence alignment, we identify pairs of homologous genes for human and mouse (17,486 gene pairs); human and rat (13,386 gene pairs); and mouse and rat (14,416 gene pairs). Within these homologous gene pairs, we distinguish homologous exons and species-specific exons. Sequences from alternatively spliced, species-specific exons were aligned with the corresponding introns in the other species to yield 767 human, 1768 mouse and 1337 rat novel shadow exons. A surprisingly large number of alternatively spliced exons remained species-specific: 5330 human, 3841 mouse and 2912 rat exons.