ArticleBioinformatics (Oxford, England)2019
Global importance of RNA secondary structures in protein-coding sequences.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT.bioRxiv : the preprint server for biology · 2026Article
- First full-genome alignment representative for the genusRNA (New York, N.Y.) · 2026Article
- Artificial intelligence in mitotic checkpoint modeling: transforming our understanding of cellular division through machine learning and predictive biology.Briefings in bioinformatics · 2026Review
- Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites.BMC cancer · 2024Article
- Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.Scientific reports · 2024Article
- Article
- Sulfonylation of RNA 2'-OH groups.ACS central science · 2023Article
- Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs.International journal of molecular sciences · 2022Article
- sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction.RNA biology · 2022Article
- HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection.Viruses · 2020Article
- Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication.International journal of molecular sciences · 2020Article
- Hepatitis C Virus Translation Regulation.International journal of molecular sciences · 2020Review
- Review
- Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life.Open biology · 2019Article
- Conserved Secondary Structures in Viral mRNAs.Viruses · 2019Article
- Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling.International journal of molecular sciences · 2019Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationThe protein-coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base-pairing.
resultsWe show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein-coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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