ArticleRNA (New York, N.Y.)2004
Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.
Article in RNA (New York, N.Y.), 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Single-turnover kinetic analysis of non-long terminal repeat retrotransposition defines the pathway and rate constants leading to second-strand synthesis.Nucleic acids research · 2026Article
- Biology and utilization of R2 retrotransposons.RNA biology · 2025Review
- Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein.Nucleic acids research · 2024Article
- Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription.Science (New York, N.Y.) · 2023Article
- Characterization and Evolution of Germ1, an Element that Undergoes Diminution in Lampreys (Cyclostomata: Petromyzontidae).Journal of molecular evolution · 2019Article
- Identification of RNA binding motifs in the R2 retrotransposon-encoded reverse transcriptase.Nucleic acids research · 2014Article
- Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.Journal of molecular biology · 2011Article
- Genetically tagged TRE5-A retrotransposons reveal high amplification rates and authentic target site preference in the Dictyostelium discoideum genome.Nucleic acids research · 2011Article
- Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.Biochemistry · 2011Article
- R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript.Molecular and cellular biology · 2010Article
- Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.Journal of molecular biology · 2009Article
- Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.Nucleic acids research · 2008Article
- Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure.RNA (New York, N.Y.) · 2007Article
- DMS footprinting of structured RNAs and RNA-protein complexes.Nature protocols · 2007Article
- RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.Insect molecular biology · 2006Article
- Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.BMC bioinformatics · 2006Article
- Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures.Plant physiology · 2005Article
- Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction.Nucleic acids research · 2005Article
- The R2 retrotransposon RNA families.RNA biologyArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
The RNA structure of the 3' untranslated region (UTR) of the R2 retrotransposable element is recognized by the R2-encoded reverse transcriptase in a reaction called target primed reverse transcription (TPRT). To provide insight into structure-function relationships important for TPRT, we have created alignments that reveal the secondary structure for 22 Drosophila and five silkmoth 3' UTR R2 sequences. In addition, free energy minimization has been used to predict the secondary structure for the 3' UTR R2 RNA of Forficula auricularia. The predicted structures for Bombyx mori and F. auricularia are consistent with chemical modification data obtained with beta-ethoxy-alpha-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. The structures appear to have common helices that are likely important for function.
Indexed as
Identifiers
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.