ArticleNucleic acids research2011
tRNADB-CE 2011: tRNA gene database curated manually by experts.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 98 citations in OpenAlex.
- The Evolution of the First Code.Genes · 2026Review
- Enzymology of the metazoan tRNA ligase complex: a lifetime in cycles.Cellular and molecular life sciences : CMLS · 2026Review
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- Automated orthogonal tRNA generation.Nature chemical biology · 2025Article
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- Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs.Nucleic acids research · 2022Article
- PltRNAdb: Plant transfer RNA database.PloS one · 2022Article
- Role of a cryptic tRNA gene operon in survival under translational stress.Nucleic acids research · 2021Article
- The complete mitochondrial DNA genome of a cone snail,Mitochondrial DNA. Part B, Resources · 2021Article
- Article
- Macrophage Selenoproteins Restrict Intracellular Replication ofFrontiers in immunology · 2021Article
- Article
- Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes.mSystems · 2020Article
- Niche differentiation is spatially and temporally regulated in the rhizosphere.The ISME journal · 2020Article
- Divergent Evolution of Eukaryotic CC- and A-Adding Enzymes.International journal of molecular sciences · 2020Article
- Article
- Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.Frontiers in microbiology · 2020Article
- tRNAviz: explore and visualize tRNA sequence features.Nucleic acids research · 2019Article
- AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana.Nucleic acids research · 2019Article
- The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family.PloS one · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We updated the tRNADB-CE by analyzing 939 complete and 1301 draft genomes of prokaryotes and eukaryotes, 171 complete virus genomes, 121 complete chloroplast genomes and approximately 230 million sequences obtained by metagenome analyses of 210 environmental samples. The 287 102 tRNA genes in total, and thus two times of the tRNA genes compiled previously, are compiled, in which sequence information, clover-leaf structure and results of sequence similarity and oligonucleotide-pattern search can be browsed. In order to pool collective knowledge with help from any experts in the tRNA research field, we included a column to which comments can be added on each tRNA gene. By compiling tRNAs of known prokaryotes with identical sequences, we found high phylogenetic preservation of tRNA sequences, especially at a phylum level. Furthermore, a large number of tRNAs obtained by metagenome analyses of environmental samples had sequences identical to those found in known prokaryotes. The identical sequence group, therefore, can be used as phylogenetic markers to clarify the microbial community structure of an ecosystem. The updated tRNADB-CE provided functions, with which users can obtain the phylotype-specific markers (e.g. genus-specific markers) by themselves and clarify microbial community structures of ecosystems in detail. tRNADB-CE can be accessed freely at http://trna.nagahama-i-bio.ac.jp.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.