Genome annotation projects are producing gene sets saturated with alternative splicing variants (11). If alternative splicing does have the potential to expand the cellular functional repertoire in eukaryotic species, it would seem to be important to assign roles to these splicing variants. However, the sheer quantity of genomic data generated by these projects (12,13) presents serious challenges for functional annotation. At present, almost all the experimental information related to alternative coding variants has been generated for RNA transcripts rather than protein isoforms. Despite the fact that there is only piecemeal experimental data for the cellular role of alternative isoforms, it is possible to predict the likely biological effects of alternative splicing.
