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

Nature. 2002 Dec 5;420(6915):563-73. doi: 10.1038/nature01266.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics
  • Amino Acid Motifs
  • Animals
  • Chromosomes, Mammalian / genetics
  • Cloning, Molecular
  • DNA, Complementary / genetics*
  • Databases, Genetic
  • Expressed Sequence Tags
  • Genes / genetics
  • Genomics* / methods
  • Humans
  • Membrane Proteins / genetics
  • Mice / genetics*
  • Physical Chromosome Mapping
  • Protein Structure, Tertiary
  • Proteome / chemistry
  • Proteome / genetics
  • RNA, Antisense / genetics
  • RNA, Messenger / analysis
  • RNA, Messenger / genetics
  • RNA, Untranslated / analysis
  • RNA, Untranslated / genetics
  • Transcription Initiation Site
  • Transcription, Genetic / genetics*


  • DNA, Complementary
  • Membrane Proteins
  • Proteome
  • RNA, Antisense
  • RNA, Messenger
  • RNA, Untranslated