title: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
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.
authors.affiliation: [1] Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D020816:Amino Acid Motifs; D000818:Animals; D033481:Chromosomes, Mammalian / Q000235:genetics; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005796:Genes / Q000235:genetics; D023281:Genomics / Q000379:methods; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics; D051379:Mice / Q000235:genetics*; D020161:Physical Chromosome Mapping; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D016372:RNA, Antisense / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D022661:RNA, Untranslated / Q000032:analysis / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D008565:Membrane Proteins; D020543:Proteome; D016372:RNA, Antisense; D012333:RNA, Messenger; D022661:RNA, Untranslated