Spliceosome assembly and/or splicing of a nascent transcript may be crucial for 
proper isoform expression and gene regulation in higher eukaryotes. We recently 
showed that cotranscriptional splicing occurs efficiently in Drosophila, but 
there are not comparable genome-wide nascent splicing data from mammals. To 
provide this comparison, we analyze a recently generated, high-throughput 
sequencing data set of mouse liver nascent RNA, originally studied for circadian 
transcriptional regulation. Cotranscriptional splicing is approximately twofold 
less efficient in mouse liver than in Drosophila, i.e., nascent intron levels 
relative to exon levels are ∼0.55 in mouse versus 0.25 in the fly. An additional 
difference between species is that only mouse cotranscriptional splicing is 
optimal when 5'-exon length is between 50 and 500 bp, and intron length does not 
correlate with splicing efficiency, consistent with exon definition. A similar 
analysis of intron and exon length dependence in the fly is more consistent with 
intron definition. Contrasted with these differences are many similarities 
between the two systems: Alternatively annotated introns are less efficiently 
spliced cotranscriptionally than constitutive introns, and introns of 
single-intron genes are less efficiently spliced than introns from multi-intron 
genes. The most striking common feature is intron position: Cotranscriptional 
splicing is much more efficient when introns are far from the 3' ends of their 
genes. Additionally, absolute gene length correlates positively with 
cotranscriptional splicing efficiency independently of intron location and 
position, in flies as well as in mice. The gene length and distance effects 
indicate that more "nascent time" gives rise to greater cotranscriptional 
splicing efficiency in both systems.