ArticleGenome biology2008
Cross-kingdom patterns of alternative splicing and splice recognition.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed, 152 citations in OpenAlex.
- Probing the genomic and proteomic basis of encystment inmSystems · 2026Article
- Omics-based dissection of alternative splicing and the regulatory architecture in fungal genomes.Current research in microbial sciences · 2026Review
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3.Journal of molecular evolution · 2025Article
- Transcriptomic Analysis Reveals Molecular Mechanisms Underpinning Mycovirus-Mediated Hypervirulence inJournal of fungi (Basel, Switzerland) · 2025Article
- Identification of Splicing Variation Associated with Parental Behavior in the Burying Beetles (Journal of genomics · 2025Article
- Drosophila Topoisomerase 3β binds to mRNAs in vivo, contributes to their localization and stability, and counteracts premature aging.PloS one · 2025Article
- Article
- Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.Nature communications · 2024Article
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- Importance of pre-mRNA splicing and its study tools in plants.Advanced biotechnology · 2024Review
- Comprehensive analysis of splicing factor SRs-related gene characteristics: predicting osteosarcoma prognosis and immune regulation status.Frontiers in oncology · 2024Article
- Regulation of Flowering Time and Other Developmental Plasticities by 3' Splicing Factor-Mediated Alternative Splicing inPlants (Basel, Switzerland) · 2023Review
- Alternative Splicing Analysis Revealed the Role of Alpha-Linolenic Acid and Carotenoids in Fruit Development ofInternational journal of molecular sciences · 2023Article
- Article
- New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data.BMC genomics · 2022Article
- Derivation of splice junction-specific antibodies using a unique hapten targeting strategy and directed evolution.New biotechnology · 2022Article
- Dynamic Transcriptional Landscape of Grass Carp (International journal of molecular sciences · 2022Article
- Intronization Signatures in Coding Exons Reveal the Evolutionary Fluidity of Eukaryotic Gene Architecture.Microorganisms · 2022Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundVariations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized.
resultsAll eukaryotes we studied exhibit RIs, which appear more frequently than previously thought. CEs are also present in all kingdoms and most of the organisms in our analysis. We observe that the ratio of CEs to RIs varies substantially among kingdoms, while the ratio of competing 3' acceptor and competing 5' donor sites remains nearly constant. In addition, we find the ratio of CEs to RIs in each organism correlates with the length of its introns. In all 14 fungi we examined, as well as in most of the 9 protists, RIs far outnumber CEs. This differs from the trend seen in 13 multicellular animals, where CEs occur much more frequently than RIs. The six plants we analyzed exhibit intermediate proportions of CEs and RIs.
conclusionOur results suggest that most extant eukaryotes are capable of recognizing splice sites via both ID and ED, although ED is most common in multicellular animals and ID predominates in fungi and most protists.
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Registered trials
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