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The PlantRNA database compiles tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. This database is hosted and maintained by the Plant Molecular Biology Institute (IBMP) of Strasbourg (http://www.ibmp.cnrs.fr/).
The PlantRNA database provides, in addition to tRNA gene sequences with their (linear) secondary structure, other important biological information on:
5'- and 3'- flanking sequences
tRNA intron sequences
sites of transcription initiation and poly(T) stretches thought to act as transcription terminators
sequences of A and B boxes involved in TFIIIC (Transcription factor for Polymerase III) binding
aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation (RNase P, RNase Z, tRNA-nucleotidyl transferase
and other tRNA modification enzymes)
tRNA import into mitochondria
references to published articles
Currently, the PlantRNA database contains genome wide information concerning five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula, Brachypodium dystachyon), a bryophyte (Physcomitrella patens), a glaucophyte (Cyanophora paradoxa), two green algae (Chlamydomonas reinhardtii, Ostreococcus tauri), a brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The set of annotated tRNA gene sequences has been manually curated and is as confident as possible (Michaud et al., 2011, Plant J. 66: 80-93 and unpublished data). In the future, the PlantRNA database will be regularly updated and implemented with tRNA annotations from new fully sequenced plant genomes.
Please cite the reference below in publications when using the PlantRNA database.
Cognat V.*, Pawlak G.*, Duchêne A.M., Daujat M., Gigant A., Salinas T., Michaud M., Gutmann B., Giegé P., Gobert A. and Maréchal-Drouard L.
PlantRNA, a database for tRNAs of photosynthetic eukaryotes.
Nucleic Acids Res. (2013) 41(D1): D273-D279, doi: 10.1093/nar/gks935, abstract
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