ArticleNucleic acids research2008
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 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.
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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
142 citing papers in PubMed, 219 citations in OpenAlex.
- H/ACA snoRNAs and snoRNPs Dysregulation Links rRNA Modification to Glioblastoma Progression.Research square · 2025Article
- Epitranscriptomic modifications in plant RNAs.RNA biology · 2025Review
- Computational limitations and future needs to unravel the full potential of 2'-O-methylation and C/D box snoRNAs.RNA biology · 2025Review
- Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.Cell reports methods · 2025Article
- Determination of Differential miRNA Expression Profile in People with Noise-Induced Hearing Loss.International journal of molecular sciences · 2025Article
- An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation.Molecular cell · 2025Article
- Ribosomes: from conserved origin to functional/medical mobility and heterogeneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Impacts of ribosomal RNA sequence variation on gene expression and phenotype.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- SNORD113-114 cluster maintains haematopoietic stem cell self-renewal via orchestrating the translation machinery.Nature cell biology · 2025Article
- Pseudouridine guides germline small RNA transport and epigenetic inheritance.Nature structural & molecular biology · 2025Article
- The Ptch/SPOUT1 methyltransferase deposits an mScience advances · 2024Article
- Article
- RNA tertiary structure and conformational dynamics revealed by BASH MaP.bioRxiv : the preprint server for biology · 2024Article
- The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA.Nature structural & molecular biology · 2024Article
- MODOMICS: a database of RNA modifications and related information. 2023 update.Nucleic acids research · 2024Article
- The RNA-Binding Function of Ribosomal Proteins and Ribosome Biogenesis Factors in Human Health and Disease.Biomedicines · 2023Review
- METTL5-mediated 18S rRNA mMolecular therapy : the journal of the American Society of Gene Therapy · 2023Article
- NCellular & molecular biology letters · 2023Review
- Article
- Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2'-O-methylation.Cell research · 2023Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/
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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.