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Nucleic Acids Research 2006 34(Database Issue):D125-D130; doi:10.1093/nar/gkj081
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Nucleic Acids Research, 2006, Vol. 34, Database issue D125-D130
© The Author 2006. 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}oxfordjournals.org

Article

IRESite: the database of experimentally verified IRES structures (www.iresite.org)

Martin Mokrejs1,2, Václav Vopálensky1, Ondrej Kolenaty1, Tomás Masek1, Zuzana Feketová1, Petra Sekyrová3, Barbora Skaloudová1, Vítezslav Kríz4 and Martin Pospísek1,5,*

1Charles University, Faculty of Science, Department of Genetics and Microbiology Vinicna 5, Prague 2, 128 44, Czech Republic 2Bioinformatics, Donovalska 1658 Prague 4, 149 00, Czech Republic 3University of South Bohemia, Faculty of Biological Sciences, Department of Molecular Biology Branisovska 31, Ceske Budejovice 370 05, Czech Republic 4Technical University of Liberec, Faculty of Mechatronics and Interdisciplinary Engineering Studies, Department of Software Engineering Halkova 6, Liberec 461 17, Czech Republic 5Charles University, 2nd Faculty of Medicine, Clinic of Paediatric Haematology and Oncology V Uvalu 84, Prague 5, 150 06, Czech Republic

*To whom correspondence should be addressed. Tel: +420 221951719; Fax: +420 221951724; Email: martin{at}natur.cuni.cz

Received August 15, 2005. Revised October 11, 2005. Accepted October 11, 2005.

IRESite is an exhaustive, manually annotated non-redundant relational database focused on the IRES elements (Internal Ribosome Entry Site) and containing information not available in the primary public databases. IRES elements were originally found in eukaryotic viruses hijacking initiation of translation of their host. Later on, they were also discovered in 5'-untranslated regions of some eukaryotic mRNA molecules. Currently, IRESite presents up to 92 biologically relevant aspects of every experiment, e.g. the nature of an IRES element, its functionality/defectivity, origin, size, sequence, structure, its relative position with respect to surrounding protein coding regions, positive/negative controls used in the experiment, the reporter genes used to monitor IRES activity, the measured reporter protein yields/activities, and references to original publications as well as cross-references to other databases, and also comments from submitters and our curators. Furthermore, the site presents the known similarities to rRNA sequences as well as RNA–protein interactions. Special care is given to the annotation of promoter-like regions. The annotated data in IRESite are bound to mostly complete, full-length mRNA, and whenever possible, accompanied by original plasmid vector sequences. New data can be submitted through the publicly available web-based interface at http://www.iresite.org and are curated by a team of lab-experienced biologists.

Correspondence may also be addressed to Martin Mokrejs. Tel/Fax: +420 272928601; Email: mmokrejs{at}iresite.org


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