The international FANTOM consortium aims to produce a comprehensive picture of 
the mammalian transcriptome, based upon an extensive cDNA collection and 
functional annotation of full-length enriched cDNAs. The previous dataset, 
FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation 
revealed that this cDNA dataset contained only about half of the estimated 
number of mouse protein-coding genes, indicating that a number of cDNAs still 
remained to be collected and identified. To pursue the complete gene catalog 
that covers all predicted mouse genes, cloning and sequencing of full-length 
enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly 
isolated cDNAs were subjected to functional annotation, and the annotation of 
4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, 
we improved our automated annotation pipeline by introducing new coding sequence 
prediction programs and developed a Web-based annotation interface for 
simplifying the annotation procedures to reduce manual annotation errors. 
Automated coding sequence and function prediction was followed with manual 
curation and review by expert curators. A total of 102,801 full-length enriched 
mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally 
annotated as protein coding (including partial or truncated transcripts), 
providing to our knowledge the greatest current coverage of the mouse proteome 
by full-length cDNAs. The total number of distinct non-protein-coding 
transcripts increased to 34,030. The FANTOM3 annotation system, consisting of 
automated computational prediction, manual curation, and final expert curation, 
facilitated the comprehensive characterization of the mouse transcriptome, and 
could be applied to the transcriptomes of other species.