Systematic evaluation of isoform function in literature reports of alternative splicing

ABSTRACT Although most mammalian genes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the genome’s functional repertoire. To ground this debate in data, we established a curation framework for evaluating experimental evidence of functionally distinct splice isoforms (FDSIs) and analyzed splice isoform function for over 700 human and mouse genes. Despite our bias towards prominently studied genes, we found experimental evidence meeting the classical definition for functionally distinct isoforms for only ~5% of the curated genes. If we relax our criteria, the fraction of genes with support for FDSIs remains low (~13%). We provide evidence that this picture will not change substantially with further curation. Furthermore, many FDSIs did not trace to a specific isoform in Ensembl. Our work has implications for computational analyses of alternative splicing and should help shape research around the role of splicing on gene function from presuming large general effects to acknowledging the need for stronger experimental evidence.