Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.

TitleIdentification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.
Publication TypeJournal Article
Year of Publication2004
AuthorsWu, JQian, Shteynberg, D, Arumugam, M, Gibbs, RA, Brent, MR
JournalGenome Res
Date Published2004 Apr
KeywordsAnimals, Computational Biology, Genes, Humans, Introns, Open Reading Frames, Predictive Value of Tests, Rats, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Software, Untranslated Regions

The publication of a draft sequence of a third mammalian genome--that of the rat--suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive annotation efforts that are currently being devoted to human. In this paper, we demonstrate an alternative approach: reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing based on dual-genome de novo predictions from TWINSCAN. We tested 444 TWINSCAN-predicted rat genes that showed significant homology to known human genes implicated in disease but that were partially or completely missed by methods based on protein-to-genome mapping. Using primers in exons flanking a single predicted intron, we were able to verify the existence of 59% of these predicted genes. We then attempted to amplify the complete predicted open reading frames of 136 genes that were verified in the single-intron experiment. Spliced sequences were amplified in 46 cases (34%). We conclude that this procedure for elucidating gene structures with native cDNA sequences is cost-effective and will become even more so as it is further optimized.

Alternate JournalGenome Res.
PubMed ID15060008
PubMed Central IDPMC383311
Grant ListR01 HG002278 / HG / NHGRI NIH HHS / United States