NAR Molecular Biology Database Collection entry number 1019
Chaparro C.1, Guyot R.1, Zuccolo A.2, PiÃ©gu B.1 and Panaud O.1
1 Laboratoire GÃ©nome et DÃ©veloppement des Plantes, UMR 5096 CNRS-IRD-UniversitÃ© de Perpignan. 52, avenue Paul Alduy. 66860 Perpignan. France2 Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
With the availability of the complete genomic sequence of rice, the identification and annotation of LTR-Retrotransposons has become a necessity as they comprise an important part of plant genomes (1). RetrOryza is a database that aims at providing the research community with the most complete resource on LTR-retrotransposon for rice. We provide the full description of 242 families of retrotransposons which have been curated and functionally annotated, this includes the identification of the Primer Binding Site, the PolyPurine Tract, the Target Site Duplication and the region matching a polyprotein when posible. The web interface allows the database to be browsed in an user friendly manner and some services are made available, such as a tool allowing the search of LTR-retrotransposons in the neighborhood of a gene of interest (based on the TIGR pseudomolecule annotation). Another service is the possibility to annotate a raw genomic sequence from any rice variety. A gff file describing the precise annotation of all LTR-retrotransposons will be returned which can be opened with any annotation tool or spreadsheet application.
C. Chaparro is funded by the ITEGE project (ANR-05-BLAN-0244-03). The work is supported by both ANR and CNRS.
1. Kumar, A. and Bennetzen, J.L. (1999). Plant retrotransposons. Annu Rev Genet, 33, 479-532.
Category: Nucleotide Sequence Databases
Subcategory: Coding and non-coding DNA
Category: Plant databases
Go to the abstract in the NAR 2007 Database Issue.
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