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The mammalian transcriptome

60,000 full-length mRNA transcripts from the mouse genome cloned and characterized.

Jonathan Weitzman(jonathanweitzman@hotmail.com)

In the December 5 Nature, the FANTOM Consortium and the RIKEN Genome Exploration Groups report a comprehensive characterization of the mouse transcriptome (Nature, 420:563-573, December 5, 2002).

Only a small proportion of the mouse genome is transcribed into functional readouts – protein-coding and non-coding mRNAs. The Japanese initiative is a large-scale project to sequence full-length mouse cDNAs for functional annotation. The FANTOM2 clone set contains 60,770 cDNAs of which around 21,000 clones have been previously reported. The term "transcriptional unit" (TU) is used to avoid complications arising from alternative splicing that generates proteins with different sequences. Most clones come from cDNA libraries from C57BL/6J mice (the strain used by the Mouse Genome Sequencing Consortium).

Computational analysis reduced the clones to 33,409 representative transcript clusters, around of half of which were predicted to code for proteins. Around 41% of transcripts showed evidence of alternative splicing, and splicing...

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