Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

FANTOM Consortium, Y Okazaki, M Furuno, T Kasukawa, J Adachi, H Bono, S Kondo, I Nikaido, N Osato, R Saito, H Suzuki, I Yamanaka, H Kiyosawa, K Yagi, Y Tomaru, Y Hasegawa, A Nogami, C Schönbach, T Gojobori, R BaldarelliD P Hill, C Bult, D A Hume, J Quackenbush, L M Schriml, A Kanapin, H Matsuda, S Batalov, K W Beisel, J A Blake, D Bradt, V Brusic, C Chothia, L E Corbani, S Cousins, E Dalla, T A Dragani, C F Fletcher, A Forrest, K S Frazer, T Gaasterland, M Gariboldi, C Gissi, A Godzik, J Gough, S Grimmond, S Gustincich, I J Jackson, C Schneider, C A M Semple, M S Taylor

Research output: Contribution to journalArticlepeer-review


Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Original languageEnglish
Pages (from-to)563-73
Number of pages11
Issue number6915
Publication statusPublished - 2002


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