PlantRNA


36196656	PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes. [PMID: 36196656] Valérie Cognat, Gael Pawlak, David Pflieger, Laurence Drouard Abstract PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. tRNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, about 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T-regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included. Plant J. 2022:112(4) \| 11 Citations (from Europe PMC, 2025-03-22)
23066098	PlantRNA, a database for tRNAs of photosynthetic eukaryotes. [PMID: 23066098] Cognat V, Pawlak G, Duchêne AM, Daujat M, Gigant A, Salinas T, Michaud M, Gutmann B, Giegé P, Gobert A, Maréchal-Drouard L. Abstract PlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community. Nucleic Acids Res. 2013:41(Database issue) \| 37 Citations (from Europe PMC, 2025-03-22)

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes. [PMID: 36196656]

Valérie Cognat, Gael Pawlak, David Pflieger, Laurence Drouard

PlantRNA (http://plantrna.ibmp.cnrs.fr/) is a comprehensive database of transfer RNA (tRNA) gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms. In the first release (PlantRNA 1.0), tRNA genes from 11 organisms were annotated. In this second version, the annotation was implemented to 51 photosynthetic species covering the whole phylogenetic tree of photosynthetic organisms, from the most basal group of Archeplastida, the glaucophyte Cyanophora paradoxa, to various land plants. tRNA genes from lower photosynthetic organisms such as streptophyte algae or lycophytes as well as extremophile photosynthetic species such as Eutrema parvulum were incorporated in the database. As a whole, about 37 000 tRNA genes were accurately annotated. In the frame of the tRNA genes annotation from the genome of the Rhodophyte Chondrus crispus, non-canonical splicing sites in the D- or T-regions of tRNA molecules were identified and experimentally validated. As for PlantRNA 1.0, comprehensive biological information including 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences and tRNA mitochondrial import are included.

Plant J. 2022:112(4) | 11 Citations (from Europe PMC, 2025-03-22)

PlantRNA, a database for tRNAs of photosynthetic eukaryotes. [PMID: 23066098]

Cognat V, Pawlak G, Duchêne AM, Daujat M, Gigant A, Salinas T, Michaud M, Gutmann B, Giegé P, Gobert A, Maréchal-Drouard L.

Abstract

PlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community.

Nucleic Acids Res. 2013:41(Database issue) | 37 Citations (from Europe PMC, 2025-03-22)

URL:	http://plantrna.ibmp.cnrs.fr/
Full name:
Description:	PlantRNA database compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear,plastidial and mitochondrial genomes.
Year founded:	2013
Last update:	2021
Version:	v2.0
Accessibility:	Accessible
Country/Region:	France

Data type:	RNA
Data object:	Plant
Database category:	Gene genome and annotation
Major species:	Arabidopsis thaliana Oryza sativa Populus trichocarpa Medicago truncatula Brachypodium distachyon Physcomitrella patens Chlamydomonas reinhardtii Ostreococcus tauri Cyanophora paradoxa Ectocarpus siliculosus Phaeodactylum tricornutum
Keywords:	tRNA

University/Institution:	University of Strasbourg
Address:	12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
City:	Strasbourg
Province/State:
Country/Region:	France
Contact name (PI/Team):	Laurence Drouard
Contact email (PI/Helpdesk):	laurence.drouard@ibmp-cnrs.unistra.fr

Database Commons
a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Research & Resources

Featured

Alliance & Collaboration

Conference & Outreach

About

Database Commons a catalog of worldwide biological databases