ArticleNAR genomics and bioinformatics2021
Quantifying splice-site usage: a simple yet powerful approach to analyze splicing.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 25 citations in OpenAlex.
- Multiple quality control checkpoints safeguard small nuclear RNA biogenesis and prevent assembly of aberrant spliceosomes.Genes & development · 2026Article
- Advances and challenges of splicing prediction with AI.Nature genetics · 2026Review
- SpliceSelectNet: a hierarchical Transformer-based deep learning model for splice site prediction.Nucleic acids research · 2026Article
- Improving splice site usage prediction with SPLAIRE.bioRxiv : the preprint server for biology · 2026Article
- Article
- Multiple Quality Control Checkpoints Safeguard Small Nuclear RNA Biogenesis and Prevent Assembly of Aberrant Spliceosomes.bioRxiv : the preprint server for biology · 2025Article
- A basic framework to explain splice-site choice in eukaryotes.Nature communications · 2025Article
- Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis.Genome biology · 2025Article
- Simple sequence repeats and their expansions: role in plant development, environmental response and adaptation.The New phytologist · 2025Review
- Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads.Genome research · 2025Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- SpliceTransformer predicts tissue-specific splicing linked to human diseases.Nature communications · 2024Article
- SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.bioRxiv : the preprint server for biology · 2024Article
- A dual-subcellular localized β-glucosidase confers pathogen and insect resistance without a yield penalty in maize.Plant biotechnology journal · 2024Article
- Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction.Briefings in bioinformatics · 2024Article
- Do not panic: An intron-centric guide to alternative splicing.The Plant cell · 2023Review
- Predicting RNA splicing from DNA sequence using Pangolin.Genome biology · 2022Article
- Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits.American journal of human genetics · 2022Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms (1-3). Regulation of splicing occurs through differential selection of splice sites in a splicing reaction, which results in variation in the abundance of isoforms and/or splicing events. However, genomic determinants that influence splice-site selection remain largely unknown. While traditional approaches for analyzing splicing rely on quantifying variant transcripts (i.e. isoforms) or splicing events (i.e. intron retention, exon skipping etc.) (4), recent approaches focus on analyzing complex/mutually exclusive splicing patterns (5-8). However, none of these approaches explicitly measure individual splice-site usage, which can provide valuable information about splice-site choice and its regulation. Here, we present a simple approach to quantify the empirical usage of individual splice sites reflecting their strength, which determines their selection in a splicing reaction. Splice-site strength/usage, as a quantitative phenotype, allows us to directly link genetic variation with usage of individual splice-sites. We demonstrate the power of this approach in defining the genomic determinants of splice-site choice through GWAS. Our pilot analysis with more than a thousand splice sites hints that sequence divergence in
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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.