PlantRNA
The PlantRNA database compiles tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. For each tRNA gene, the linear secondary structure is given as well as biological information. 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. Data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA binding proteins are also included.
Description
More detailed information about this field from each metasource.
The PlantRNA database compiles tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. For each tRNA gene, the linear secondary structure is given as well as biological information. 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. Data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA binding proteins are also included.
metasource: Fairsharing.orgversion: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The PlantRNA database compiles 4,375 tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. To the manually curated lists of tRNA genes that we recently extracted from the genomes of five angiosperms (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula, Brachypodium distachyon) and one green alga (Chlamydomonas reinhardtii) (1), we retrieved tRNA genes from the genomes of 6 other photosynthetic organisms, namely another green alga (Ostreococcus tauri), a glaucophyte (Cyanophora paradoxa), a brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). Whole genomes were scanned by tRNAscan-SE (2) and then manually annotated as described in (1). For each tRNA gene, the linear secondary structure is given as well as biological information. 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. Due to the importance of the dual-targeting phenomenon for proteins involved in translation in plants (3), we also put strong effort in providing the subcellular localization of these enzymes. Finally, data on mitochondrial import (3) of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA binding proteins are also included. Transfer RNA gene sequences and optional information can be downloaded in xls or FASTA file formats. In addition, a SQL dump of the database is available upon request.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://plantrna.ibmp.cnrs.fr/Webpage
More detailed information about this field from each metasource.
http://plantrna.ibmp.cnrs.fr/
metasource: Fairsharing.orgversion: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
A global picture of tRNA genes in plant genomes
PMID: 21443625
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
PMID: 23066098
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gks935
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
A global picture of tRNA genes in plant genomes
PMID: 21443625
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
PMID: 23066098
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gks935
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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A global picture of tRNA genes in plant genomes
PubMed citations: 45.
45 articles citing: A global picture of tRNA genes in plant genomes
PtRNAdb: a web resource of plant tRNA genes from a wide range of plant species. PMID:35875176
Mitochondrial genome of Garcinia mangostana L. variety Mesta. PMID:35676406
Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants. PMID:35587610
Codon usage bias. PMID:34822069
Evolution and structural variations in chloroplast tRNAs in gymnosperms. PMID:34663228
Intragenic tRNA-promoted R-loops orchestrate transcription interference for plant oxidative stress responses. PMID:34463741
Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss. PMID:34436590
Plant Small RNA World Growing Bigger: tRNA-Derived Fragments, Longstanding Players in Regulatory Processes. PMID:34164429
Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. PMID:34159889
Structural variation and evolution of chloroplast tRNAs in green algae. PMID:34131524
Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants. PMID:34059643
On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? PMID:33796548
Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. PMID:33569675
Epigenetic silencing of clustered tRNA genes in Arabidopsis. PMID:32941623
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. PMID:32932872
The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PMID:32806552
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. PMID:32448240
Recent advances in understanding mitochondrial genome diversity. PMID:32399193
Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life. PMID:32344921
LC-MS/MS Profiling of Post-Transcriptional Modifications in Ginseng tRNA Purified by a Polysaccharase-Aided Extraction Method. PMID:32316488
Comprehensive genomic analyses with 115 plastomes from algae to seed plants: structure, gene contents, GC contents, and introns. PMID:32200544
The Arabidopsis TRM61/TRM6 complex is a bona fide tRNA N1-methyladenosine methyltransferase. PMID:32095811
RNA Rings Strengthen Hairpin Accretion Hypotheses for tRNA Evolution: A Reply to Commentaries by Z.F. Burton and M. Di Giulio. PMID:32025759
Environmental and epigenetic regulation of Rider retrotransposons in tomato. PMID:31525177
LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing. PMID:31486704
The cellular landscape of mid-size noncoding RNA. PMID:30843375
How the intracellular partitioning of tRNA and tRNA modification enzymes affects mitochondrial function. PMID:30358065
Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea. PMID:29930548
accD nuclear transfer of Platycodon grandiflorum and the plastid of early Campanulaceae. PMID:28800729
Analyses of Genomic tRNA Reveal Presence of Novel tRNAs in Oryza sativa. PMID:28713421
The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. PMID:27899576
Phylogenetic distribution of plant snoRNA families. PMID:27881081
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. PMID:27515907
Differential substrate recognition by isozymes of plant protein-only Ribonuclease P. PMID:26966150
Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae. PMID:26268215
Extensive tRNA gene changes in synthetic Brassica napus. PMID:24271856
Mitochondrial Genome Sequence of the Legume Vicia faba. PMID:23675376
PlantRNA, a database for tRNAs of photosynthetic eukaryotes. PMID:23066098
Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PMID:22952830
The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules. PMID:22922796
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PMID:22638584
Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine. PMID:22553362
PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis. PMID:22549728
Clustered organization, polycistronic transcription, and evolution of modification-guide snoRNA genes in Euglena gracilis. PMID:22134850
A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2. PMID:21781332 -
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
PubMed citations: 31.
31 articles citing: PlantRNA, a database for tRNAs of photosynthetic eukaryotes
PtRNAdb: a web resource of plant tRNA genes from a wide range of plant species. PMID:35875176
PltRNAdb: Plant transfer RNA database. PMID:35605006
Characterization of Frond and Flower Development and Identification of FT and FD Genes From Duckweed Lemna aequinoctialis Nd. PMID:34707626
On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? PMID:33796548
The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies. PMID:33575626
Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. PMID:33569675
Epigenetic silencing of clustered tRNA genes in Arabidopsis. PMID:32941623
The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PMID:32806552
Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification. PMID:32715941
Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life. PMID:32344921
The Functions of Chloroplast Glutamyl-tRNA in Translation and Tetrapyrrole Biosynthesis. PMID:32071153
Arabidopsis tRNA-derived fragments as potential modulators of translation. PMID:31994438
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. PMID:30531940
Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana Protein-Only RNase P Isoenzymes. PMID:30414965
Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in Capsicum spp. PMID:30060137
In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection. PMID:29058618
Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes. PMID:28499021
The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. PMID:28369540
The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. PMID:27899576
Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. PMID:27806710
The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions. PMID:27187488
Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P. PMID:26896801
Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection. PMID:26719261
Codon reassignment to facilitate genetic engineering and biocontainment in the chloroplast of Chlamydomonas reinhardtii. PMID:26471875
Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae. PMID:26268215
The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene. PMID:25955637
Multiple RNA processing defects and impaired chloroplast function in plants deficient in the organellar protein-only RNase P enzyme. PMID:25793367
tRNA biology in mitochondria. PMID:25734984
Handling tRNA introns, archaeal way and eukaryotic way. PMID:25071838
High-throughput sequencing reveals small RNAs involved in ASGV infection. PMID:24998458 - http://dx.doi.org/10.1093/nar/gks935
Tags:
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nucleus
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plastid
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transfer rna
metasource: Fairsharing.org
version: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
nucleus
metasource: Fairsharing.orgversion: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
plastid
metasource: Fairsharing.orgversion: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
transfer rna
metasource: Fairsharing.orgversion: FAIRsharing.org: PlantRNA; PlantRNA; DOI: https://doi.org/10.25504/FAIRsharing.fy2ebk; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
rna sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
nucleus plastid transfer rna rna sequence
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