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Nucleic Acids Research 2005 33(6):1935-1939; doi:10.1093/nar/gki328
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Published online 4 April 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes

Robert Castelo*, Alexandre Reymond1,2, Carine Wyss1, Francisco Câmara, Genís Parra, Stylianos E. Antonarakis1, Roderic Guigó and Eduardo Eyras

Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra, Centre de Regulació Genòmica E08003 Barcelona, Spain 1Department of Genetic Medicine and Development, University of Geneva, Medical School and University Hospital of Geneva CMU, 1, rue Michel Servet, 1211 Geneva, Switzerland 2Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland

*To whom correspondence should be addressed. Tel: +34 932 240 884; Fax: +34 32 240 875; Email: rcastelo{at}imim.es

Received December 2, 2004. Revised December 13, 2004. Accepted March 8, 2005.

The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using comparative gene finding followed by experimental verification of exon pairs by RT–PCR, that the addition to the multi-exonic subset of this catalog could be as little as 0.2%, suggesting that we may be closing in on the human gene set. Our protocol, however, has two shortcomings: (i) the bioinformatic screening of the predicted genes, applied to filter out false positives, cannot handle intronless genes; and (ii) the experimental verification could fail to identify expression at a specific developmental time. This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes.


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