This study mapped over 200 million three-prime end reads to identify 62,032 polyadenylation sites in D. melanogaster, as well as the most common polyadenylation signal motifs. Alternative polyadenylation sites (often tissue- or stage-specific) were observed for almost two thirds of genes; three-prime UTR extensions were observed for 5,190 genes (compared to FlyBase R6.12).