This study describes comprehensive polling of transcription start and
termination sites and analysis of previously unidentified full-length complementary
DNAs derived from the mouse genome. We identify the 5¶ and 3¶
boundaries of 181,047 transcripts with extensive variation in transcripts arising
from alternative promoter usage, splicing, and polyadenylation. There are
16,247 new mouse protein-coding transcripts, including 5154 encoding
previously unidentified proteins. Genomic mapping of the transcriptome reveals
transcriptional forests, with overlapping transcription on both strands,
separated by deserts in which few transcripts are observed. The data provide
a comprehensive platform for the comparative analysis of mammalian
transcriptional regulation in differentiation and development.
