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PMID: 17071960 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

RetrOryza: a database of the rice LTR-retrotransposons.

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D66-70

Chaparro C, Guyot R, Zuccolo A, Piégu B, Panaud O

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.

MeSH Terms
Databases, Nucleic Acid Genome, Plant Genomics Internet Oryza/genetics Retroelements Terminal Repeat Sequences User-Computer Interface
Chemicals
Retroelements
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Chaparro Cristian
Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France.
Guyot Romain
Zuccolo Andrea
Piégu Benoît
Panaud Olivier
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl780
Published
2007-01-00
Epub
2006-00-28
Pages
D66-70
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1635335
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl780 PMC Full Text View journal details
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