The FANTOM Consortium and the RIKEN Genome Exploration Research Group have manually annotated 60,770 full-length mouse complementary DNA (cDNA) sequences, clustering them into 33,409 'transcriptional units' (TUs). This comprehensive survey of the mouse transcriptome includes both protein-coding and non-coding RNA transcripts, with 4,258 new protein-coding and 11,665 new non-coding messages identified. The study reveals that 41% of TUs show evidence of alternative splicing, and 2,431 sense-antisense pairs were identified. The FANTOM2 clone set, consisting of 39,694 new cDNA clones and 21,076 FANTOM1 clones, provides a valuable resource for functional genomics. The analysis of the transcriptome highlights the importance of non-coding RNAs, which constitute a significant component of the transcriptome. The study also discusses the functional annotation of proteins, the impact of alternative splicing on the proteome, and the discovery of novel genes and pathways, such as those involved in cell movement, protein metabolism, and G-protein-coupled receptors. The findings underscore the utility of the mouse as a model system for human biology and disease studies.The FANTOM Consortium and the RIKEN Genome Exploration Research Group have manually annotated 60,770 full-length mouse complementary DNA (cDNA) sequences, clustering them into 33,409 'transcriptional units' (TUs). This comprehensive survey of the mouse transcriptome includes both protein-coding and non-coding RNA transcripts, with 4,258 new protein-coding and 11,665 new non-coding messages identified. The study reveals that 41% of TUs show evidence of alternative splicing, and 2,431 sense-antisense pairs were identified. The FANTOM2 clone set, consisting of 39,694 new cDNA clones and 21,076 FANTOM1 clones, provides a valuable resource for functional genomics. The analysis of the transcriptome highlights the importance of non-coding RNAs, which constitute a significant component of the transcriptome. The study also discusses the functional annotation of proteins, the impact of alternative splicing on the proteome, and the discovery of novel genes and pathways, such as those involved in cell movement, protein metabolism, and G-protein-coupled receptors. The findings underscore the utility of the mouse as a model system for human biology and disease studies.