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Nucleic Acids Research Advance Access originally published online on October 28, 2006
Nucleic Acids Research 2007 35(Database issue):D66-D70; doi:10.1093/nar/gkl780
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Nucleic Acids Research, 2007, Vol. 35, Database issue D66-D70
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

RetrOryza: a database of the rice LTR-retrotransposons

Cristian Chaparro, Romain Guyot, Andrea Zuccolo1, Benoît Piégu and Olivier Panaud*

Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-Université de Perpignan 52 Avenue Paul Alduy, 66860 Perpignan, France 1 Department of Plant Sciences, Arizona Genomics Institute, University of Arizona Tucson, AZ 85721, USA

*To whom correspondence should be addressed. Tel: +33 468 661773; Fax: +33 468 668499; Email: panaud{at}univ-perp.fr

Received August 14, 2006. Revised September 5, 2006. Accepted October 1, 2006.

Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (http://www.retroryza.org/), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest.


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