ArticleNucleic acids research1996
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information.
Article in Nucleic acids research, 1996. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 359 papers, 4 of them syntheses that pooled it.
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Who cites it
359 citing papers in PubMed, 4 syntheses or guidelines pooled it, 818 citations in OpenAlex.
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- Meta-Analysis of Mutations inGenes · 2021Pooled it
- Association of CCND1 Gene c.870G>A Polymorphism with Breast Cancer Risk: A Case-ControlStudy and a Meta-Analysis.Pathology oncology research : POR · 2017Pooled it
- Contribution of RAD51D germline mutations in breast and ovarian cancer in Greece.Journal of human genetics · 2018Trial
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- Thyroid and breast carcinomas in a patient with Pendred syndrome: a case report and literature review.Frontiers in oncology · 2026Article
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- Immunoinformatics-based design of a multi-epitope mRNA vaccine candidate targeting the major human-infecting hepatitis E virus genotypes 1-4.Frontiers in bioinformatics · 2026Article
- Prime editing for the investigation of aberrant splicing defect associated with a pathogenicMolecular therapy. Nucleic acids · 2025Article
- Detection and validation of QTLs for flowering time in morning glory.Breeding science · 2025Article
- Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning.BMC bioinformatics · 2025Article
- VTA monosynaptic connections by local glutamate and GABA neurons and their distinct roles in behavior.Nature communications · 2025Article
- A 15 bp non-canonical splice-site deletion in ABCA4 linked with retinitis pigmentosa and myopia: insights into splicing defects and phenotypic variability.Molecular biology reports · 2025Article
- Engineering and comparison of cas12a-based genome editing systems in plants.The Plant journal : for cell and molecular biology · 2025Article
- Moderately severe osteogenesis imperfecta-like osteochondrodysplasia associated with heterozygous variants in bothJBMR plus · 2025Article
299 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local prediction of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner. The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site prediction. An analysis of the errors made by the networks in the first step of the method revealed a previously unknown feature, a frequent T-tract prolongation containing cryptic acceptor sites in the 5' end of exons. The method presented here has been compared with three other approaches, GeneFinder, Gene-Mark and Grail. Overall the method presented here is an order of magnitude better. We show that the new method is able to find a donor site in the coding sequence for the jelly fish Green Fluorescent Protein, exactly at the position that was experimentally observed in A.thaliana transformants. Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae. The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html
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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.