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Biological information
All available tRNA gene sequences from 11 photosynthetic organisms were used.
Organellar genome sequences were obtained either from GOBASE or from RefSeq
The existence of tRNAs was first predicted by using trnascan-SE version 1.2.1 with default parameters and using different sources (Mixed/Eukaryotic/Mito-Chloroplast). tRNA genes from alga obtained from SPLITSdb were also included. In addition, to minimize the number of false positives, we also manually curated the lists of tRNA genes extracted from each genome. By means of the manual curation :
we correctly annotated a few genes or pseudogenes that were misannotated
we correctly annotated numerous non-expressed mitochondrial or plastidial tRNA gene sequences inserted into nuclear genomes and
recognized by tRNAscan-SE
we re-annotated some tRNAs in terms of amino acid and codon recognition due to the presence of post-transcriptional antidocon modifications
we identified new tRNA-derives SINEs that could not be distinguished from true tRNAs by tRNAscan-SE
Organellar targeting predictions were determined with both Predotar and TargetP.
When information is not available (e.g. the mitochondrial sequence of Medicago truncatula is not known), the value "0" is given by default.
 
Please use the following link to cite the PlantRNA database: http://plantrna.ibmp.cnrs.fr/
Last update: 06/09/2012
Contributors
Name Position Email address
Valérie Cognat Engineer, CNRS valerie.cognat [at] ibmp-cnrs.unistra.fr
Magali Daujat Engineer, CNRS magali.daujat [at] ibmp-cnrs.unistra.fr
Jeanne-clotilde d'Hollander DUT student, UdS  
Laurence Drouard Research Director, CNRS laurence.drouard [at] ibmp-cnrs.unistra.fr
Anne-Marie Duchêne University lecturer, UdS anne-marie.duchene [at] ibmp-cnrs.unistra.fr
Philippe Giegé Research Director, CNRS philippe.giege [at] ibmp-cnrs.unistra.fr
Anais Gigant Engineer, CNRS  
Anthony Gobert Post-doc anthony.gobert [at] ibmp-cnrs.unistra.fr
Bernard Gutmann PhD student bernard.gutmann [at] ibmp-cnrs.unistra.fr
Morgane Michaud PhD student morgane.michaud [at] ibmp-cnrs.unistra.fr
Gael Pawlak Engineer, CNRS gael.pawlak [at] ibmp-cnrs.unistra.fr
Thalia Salinas Post-doc thalia.salinas [at] ibmp-cnrs.unistra.fr
Camille Tinguy DUT student, UdS  
Funding
Contact
For biological questions, please contact Laurence Drouard - laurence.drouard [at] ibmp-cnrs.unistra.fr
For bioinformatic questions, please contact Valérie Cognat - valerie.cognat [at] ibmp-cnrs.unistra.fr
For technical questions (standards, data structure, source request, ...), please contact Gael Pawlak - gael.pawlak [at] ibmp-cnrs.unistra.fr
SQL dump of the database is available upon request ( laurence.drouard [at] ibmp-cnrs.unistra.fr )
Libraries and technical environment
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