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Nucleic Acids Res. 2007 Jan;35(Database issue):D66-70. Epub 2006 Oct 28.

RetrOryza: a database of the rice LTR-retrotransposons.

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1
Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France.

Abstract

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.

PMID:
17071960
PMCID:
PMC1635335
DOI:
10.1093/nar/gkl780
[Indexed for MEDLINE]
Free PMC Article
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