ArticleNucleic acids research2019
RefSeq curation and annotation of stop codon recoding in vertebrates.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 50 citations in OpenAlex.
- Nonapeptide molecular evolution during the adaptive radiation of Tanganyika cichlids.Journal of neuroendocrinology · 2026Article
- Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases.PLoS computational biology · 2026Article
- Evaluating computational tools for protein-coding sequence detection: Are they up to the task?RNA (New York, N.Y.) · 2025Article
- NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.Nucleic acids research · 2025Article
- Chromosome-scale genome assembly of the hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest.G3 (Bethesda, Md.) · 2024Article
- Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator.G3 (Bethesda, Md.) · 2023Article
- Ribosome biogenesis and function in development and disease.Development (Cambridge, England) · 2023Review
- Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.BMC biology · 2021Article
- Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2.Molecular biology and evolution · 2021Article
- Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter.Scientific reports · 2021Article
- Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae.PLoS genetics · 2021Article
- Tissue-specific dynamic codon redefinition inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.Molecular biology and evolution · 2021Article
- Bioinformatics of Selenoproteins.Antioxidants & redox signaling · 2020Review
- Article
- A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms.BMC genomics · 2020Article
- Bovine Genome Database: new annotation tools for a new reference genome.Nucleic acids research · 2020Article
- MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database.Frontiers in plant science · 2020Article
- Variation benchmark datasets: update, criteria, quality and applications.Database : the journal of biological databases and curation · 2020Article
- Probing lncRNA-Protein Interactions: Data Repositories, Models, and Algorithms.Frontiers in genetics · 2019Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Recoding of stop codons as amino acid-specifying codons is a co-translational event that enables C-terminal extension of a protein. Synthesis of selenoproteins requires recoding of internal UGA stop codons to the 21st non-standard amino acid selenocysteine (Sec) and plays a vital role in human health and disease. Separately, canonical stop codons can be recoded to specify standard amino acids in a process known as stop codon readthrough (SCR), producing extended protein isoforms with potential novel functions. Conventional computational tools cannot distinguish between the dual functionality of stop codons as stop signals and sense codons, resulting in misannotation of selenoprotein gene products and failure to predict SCR. Manual curation is therefore required to correctly represent recoded gene products and their functions. Our goal was to provide accurately curated and annotated datasets of selenoprotein and SCR transcript and protein records to serve as annotation standards and to promote basic and biomedical research. Gene annotations were curated in nine vertebrate model organisms and integrated into NCBI's Reference Sequence (RefSeq) dataset, resulting in 247 selenoprotein genes encoding 322 selenoproteins, and 93 genes exhibiting SCR encoding 94 SCR isoforms.
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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.