To determine the prevalence of cotranscriptional splicing in Drosophila, we 
sequenced nascent RNA transcripts from Drosophila S2 cells as well as from 
Drosophila heads. Eighty-seven percent of the introns assayed manifest >50% 
cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced 
poorly or slowly, with ∼3% being almost completely retained in nascent pre-mRNA. 
Although individual introns showed slight but statistically significant 
differences in splicing efficiency, similar global levels of splicing were seen 
from both sources. Importantly, introns with low cotranscriptional splicing 
efficiencies are present in the same primary transcript with efficiently spliced 
introns, indicating that splicing is intron-specific. The analysis also 
indicates that cotranscriptional splicing is less efficient for first introns, 
longer introns, and introns annotated as alternative. Finally, S2 cells 
expressing the slow RpII215(C4) mutant show substantially less intron retention 
than wild-type S2 cells.