BMC Genomics Research article BioMed Central Open Access Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury Rafaela M Maia†1, Valeria Valente†1, Marco AV Cunha1, Josane F Sousa1, Daniela D Araujo1,5, Wilson A Silva Jr2, Marco A Zago3, Emmanuel Dias- Neto4,6, Sandro J Souza4, Andrew JG Simpson4,7, Nadia Monesi1,8, Ricardo GP Ramos1, Enilza M Espreafico1 and Maria L Paçó-Larson*1 Address: 1Departamento de Biologia Celular, Molecular e de Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, SP, Brazil, 2Departamento de Genética e Centro de Terapia Celular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 3900 14049-900, SP, Brazil, 3Departamento de Clínica Médica e Centro de Terapia Celular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 3900 14049-900, SP, Brazil, 4Ludwig Institute for Cancer Research, Rua Professor Antonio Prudente, 109, São Paulo 01509-010, SP, Brazil, 5DDA: Faculdade de Medicina, Universidade de Ribeirão Preto- UNAERP, Av. Costabile Romano 14096-900 Ribeirão Preto, SP, Brazil, 6EDN: Laboratório de Neurociências (LIM-27) Instituto de Psiquiatria, HCFMUSP, R. Ovidio Pires de Campos, s/n 05403-010, São Paulo, SP, Brazil and University of Texas/MD Anderson Cancer Center, 1515 Holcombe Blvd, 77030, Houston, TX, USA, 7AJGS: Ludwig Institute for Cancer Research 605 Third Avenue New York, NY 10158, USA and 8Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, SP, Brazil Email: Rafaela M Maia - rafmmaia@rbp.fmrp.usp.br; Valeria Valente - vvalente@rbp.fmrp.usp.br; Marco AV Cunha - mavcunha@bit.fmrp.usp.br; Josane F Sousa - jdfsousa@rbp.fmrp.usp.br; Daniela D Araujo - danydover@hotmail.com; Wilson A Silva - wilsonjr@usp.br; Marco A Zago - marazago@usp.br; Emmanuel Dias-Neto - emmanuel@usp.br; Sandro J Souza - sandro@compbio.ludwig.org.br; Andrew JG Simpson - asimpson@licr.org; Nadia Monesi - namonesi@fcfrp.usp.br; Ricardo GP Ramos - rgpramos@fmrp.usp.br; Enilza M Espreafico - emesprea@fmrp.usp.br; Maria L Paçó- Larson* - mlplarso@pesquisador.cnpq.br * Corresponding author †Equal contributors Published: 24 July 2007 BMC Genomics 2007, 8:249 doi:10.1186/1471-2164-8-249 This article is available from: http://www.biomedcentral.com/1471-2164/8/249 Received: 13 November 2006 Accepted: 24 July 2007 © 2007 Maia et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The sequencing of the D.melanogaster genome revealed an unexpected small number of genes (~ 14,000) indicating that mechanisms acting on generation of transcript diversity must have played a major role in the evolution of complex metazoans. Among the most extensively used mechanisms that accounts for this diversity is alternative splicing. It is estimated that over 40% of Drosophila protein-coding genes contain one or more alternative exons. A recent transcription map of the Drosophila embryogenesis indicates that 30% of the transcribed regions are unannotated, and that 1/3 of this is estimated as missed or alternative exons of previously characterized protein- coding genes. Therefore, the identification of the variety of expressed transcripts depends on experimental data for its final validation and is continuously being performed using different approaches. We applied the Open Reading Frame Expressed Sequence Tags (ORESTES) methodology, which is capable of generating cDNA data from the central portion of rare transcripts, in order to investigate the presence of hitherto unnanotated regions of Drosophila transcriptome. Page 1 of 9 (page number not for citation purposes)