ArticleGenes2018
RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.
Article in Genes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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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Who cites it
11 citing papers in PubMed, 20 citations in OpenAlex.
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- PERFUMES: pipeline to extract RNA functional motifs and exposed structures.Bioinformatics (Oxford, England) · 2024Article
- Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis.PloS one · 2024Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- m6A-related lncRNAs are potential biomarkers for the prognosis of COAD patients.Frontiers in oncology · 2022Article
- G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum.Nucleic acids research · 2021Article
- Decoding LncRNAs.Cancers · 2021Review
- Review
- SSS-test: a novel test for detecting positive selection on RNA secondary structure.BMC bioinformatics · 2019Article
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Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
In this work, we present a computational screen conducted for functional RNA structures, resulting in over 100,000 conserved RNA structure elements found in alignments of mouse (mm10) against 59 other vertebrates. We explicitly included masked repeat regions to explore the potential of transposable elements and low-complexity regions to give rise to regulatory RNA elements. In our analysis pipeline, we implemented a four-step procedure: (i) we screened genome-wide alignments for potential structure elements using RNAz-2, (ii) realigned and refined candidate loci with LocARNA-P, (iii) scored candidates again with RNAz-2 in structure alignment mode, and (iv) searched for additional homologous loci in mouse genome that were not covered by genome alignments. The 3'-untranslated regions (3'-UTRs) of protein-coding genes and small noncoding RNAs are enriched for structures, while coding sequences are depleted. Repeat-associated loci make up about 95% of the homologous loci identified and are, as expected, predominantly found in intronic and intergenic regions. Nevertheless, we report the structure elements enriched in specific genome elements, such as 3'-UTRs and long noncoding RNAs (lncRNAs). We provide full access to our results via a custom UCSC genome browser trackhub freely available on our website (http://rna.tbi.univie.ac.at/trackhubs/#RNAz).
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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.