Nature Genetics
- 38, 1151 - 1158 (2006)
Published online: 3 September 2006; Corrected online: 20 September 2006 | doi:10.1038/ng1875
Biological function of unannotated transcription during the early development of Drosophila melanogasterJ Robert Manak1, 3, Sujit Dike1, 3, Victor Sementchenko1, Philipp Kapranov1, Frederic Biemar2, Jeff Long1, Jill Cheng1, Ian Bell1, Srinka Ghosh1, Antonio Piccolboni1 & Thomas R Gingeras11
Affymetrix, Inc., Santa Clara, California, 95051, USA. 2
Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California, Berkeley, California 94720-3200, USA. 3
These authors contributed equally to this work.
Correspondence should be addressed to J Robert Manak John_Manak@affymetrix.com Many animal and plant genomes are transcribed much more extensively than current annotations predict. However, the biological function of these unannotated transcribed regions is largely unknown. Approximately 7% and 23% of the detected transcribed nucleotides during D. melanogaster embryogenesis map to unannotated intergenic and intronic regions, respectively. Based on computational analysis of coordinated transcription, we conservatively estimate that 29% of all unannotated transcribed sequences function as missed or alternative exons of well-characterized protein-coding genes. We estimate that 15.6% of intergenic transcribed regions function as missed or alternative transcription start sites (TSS) used by 11.4% of the expressed protein-coding genes. Identification of P element mutations within or near newly identified 5' exons provides a strategy for mapping previously uncharacterized mutations to their respective genes. Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome.
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