ArticlePLoS computational biology2008
A general definition and nomenclature for alternative splicing events.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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134 citing papers in PubMed.
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- Epigenetic regulation by gut microbiota-derived metabolites in celiac disease.Biochemistry and biophysics reports · 2026Review
- Systematic investigation of zinc finger MYND-type containing 11-mediated alternative splicing reveals notable events in prostate cancer.Asian journal of urology · 2026Article
- Semi-quantitative RT-PCR Assay for the Analysis of Alternative Splicing of Interleukin Genes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL.BMC plant biology · 2025Article
- Alternative splicing of bunched confers a dual role in hippo pathway-dependent growth and tumorigenesis.Oncogene · 2025Article
- Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes.Genome research · 2025Article
- Ninein isoform contributions to intracellular processes and macrophage immune function.The Journal of biological chemistry · 2025Article
- Maximal Efficacy of Alternative Splicing is Ensured by Balanced Efficiency of U1 and U2AF.bioRxiv : the preprint server for biology · 2025Article
- Difference Analysis Among Six Kinds of Acceptor Splicing Sequences by the Dispersion Features of 6-mer Subsets in Human Genes.Biology · 2025Article
- Looking beyond the ER, PR, and HER2: what's new in the ARsenal for combating breast cancer?Reproductive biology and endocrinology : RB&E · 2025Review
- Identification of Splicing Variation Associated with Parental Behavior in the Burying Beetles (Journal of genomics · 2025Article
- Alternative Splicing of Pre-mRNA Matters in Oral Diseases.Current gene therapy · 2025Review
- Profiling genetically driven alternative splicing across the Indonesian archipelago.American journal of human genetics · 2024Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- Coding, or non-coding, that is the question.Cell research · 2024Review
- junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence.NAR genomics and bioinformatics · 2024Article
- TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups.Bioinformatics (Oxford, England) · 2024Article
- Mining alternative splicing patterns in scRNA-seq data using scASfind.Genome biology · 2024Article
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3 authors.
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Abstract
Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific "AS code" to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part--in human more than a quarter-of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS.
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