ArticleScience China. Life sciences2023
Plant Intron-Splicing Efficiency Database (PISE): exploring splicing of ∼1,650,000 introns in Arabidopsis, maize, rice, and soybean from ∼57,000 public RNA-seq libraries.
Article in Science China. Life sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 13 citations in OpenAlex.
- RNA regulation in plants.Science China. Life sciences · 2026Review
- Impact of alternative splicing on Arabidopsis proteome.Nucleic acids research · 2026Article
- Comparative transcriptomic and transcript-based network analyses revealed genotype-specific alternative splicing induced by Sclerotinia sclerotiorum in Brassica napus.BMC plant biology · 2026Article
- Impact of alternative splicing on Arabidopsis proteome.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary and Structural Analysis of the Aquaporin Gene Family in Rice.Plants (Basel, Switzerland) · 2025Review
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- A Comprehensive Analysis of the Alternative Splicing Co-Factor U2AF65B Gene Family Reveals Its Role in Stress Responses and Root Development.International journal of molecular sciences · 2025Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- HDAC1: An Essential and Conserved Member of the Diverse ZnInternational journal of molecular sciences · 2023Article
- PlantIntronDB: a database for plant introns that host functional elements.Database : the journal of biological databases and curation · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
Intron retention is the most common alternative splicing event in plants and plays a crucial role in the responses of plants to environmental signals. Despite a large number of RNA-seq libraries from different treatments and genetic mutants stored in public domains, a resource for querying the intron-splicing ratio of individual intron is still required. Here, we established the first-ever large-scale splicing efficiency database in any organism. Our database includes over 57,000 plant public RNA-seq libraries, comprising 25,283 from Arabidopsis, 17,789 from maize, 10,710 from rice, and 3,974 from soybean, and covers a total of 1.6 million introns in these four species. In addition, we manually curated and annotated all the mutant- and treatment-related libraries as well as their matched controls included in our library collection, and added graphics to display intron-splicing efficiency across various tissues, developmental stages, and stress-related conditions. The result is a large collection of 3,313 treatment conditions and 3,594 genetic mutants for discovering differentially regulated splicing efficiency. Our online database can be accessed at https://plantintron.com/ .
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