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

TLDR

Only a small fraction of the mouse genome is transcribed into mature mRNAs, prompting an international effort to catalogue all full‑length transcripts in a physical clone collection. The study reports the manual annotation of 60,770 full‑length mouse cDNA sequences. Manual annotation was performed on 60,770 full‑length mouse cDNA sequences. The annotation yielded 33,409 transcriptional units, comprising 90.1 % of a new mouse transcriptome database, including 4,258 novel protein‑coding and 11,665 novel non‑coding transcripts, with 41 % showing alternative splicing—79 % of which alter protein products—and 2,431 sense–antisense pairs, making it the most comprehensive mammalian transcriptome survey to date.

Abstract

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.