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  1. RetrOryza (View Publication)
    Full Name of the Resource : LTR-retrotransposon for rice
    Resource Category : Databases -> Plant Databases -> Rice

    Brief Description : 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.
    Subject Area : LTR-retrotransposon; Rice


    Institute/s :
    Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-IRD-Universite de Perpignan. 52, avenue Paul Alduy. 66860 Perpignan, France
    Address of Institute/s :
    Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-IRD-Universite de Perpignan. 52, avenue Paul Alduy. 66860 Perpignan, France
    Country : France

    Associated Institutes :

    • Laboratoire Genome et Developpement des Plantes, UMR 5096 CNRS-IRD-Universite de Perpignan. 52, avenue Paul Alduy. 66860 Perpignan, France
    • Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA

    Associated Country : France; USA


    Authors/Contributors : Panaud, O.
    Contact Email : panaud@univ-perp.fr
    Year : 2007
    Language : English

    Keywords : Databases, Nucleic Acid; Genome, Plant; Genomics; Internet; Oryza sativa / genetics; Retroelements; Terminal Repeat Sequences; User-Computer Interface