ArticleProceedings of the National Academy of Sciences of the United States of America2001
A computational analysis of sequence features involved in recognition of short introns.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
185 citing papers in PubMed, 372 citations in OpenAlex.
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- WormTagDB: A Systematic Survey of Endogenously Tagged Proteins inbioRxiv : the preprint server for biology · 2025Article
- Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning.BMC bioinformatics · 2025Article
- Condensation of ZFP207 and U1 snRNP promotes spliceosome assembly.Nature structural & molecular biology · 2025Article
- From benign to pathogenic variants and vice versa: pyrimidine transitions at position -3 of TAG and CAG 3' splice sites.Journal of human genetics · 2025Article
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- LUC7 proteins define two major classes of 5' splice sites in animals and plants.Nature communications · 2025Article
- LINE-1 transposition into murine Thyroglobulin results in congenital thyroid dysplasia.PloS one · 2025Article
- Edited eukaryotic translation initiation factors confer resistance against maize lethal necrosis.Plant biotechnology journal · 2024Article
- RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants.International journal of molecular sciences · 2024Review
- Study of the RNA splicing kinetics via in vivo 5-EU labeling.RNA (New York, N.Y.) · 2024Article
- An interpretable model of pre-mRNA splicing for animal and plant genes.Science advances · 2024Article
- Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.RNA (New York, N.Y.) · 2024Article
- Exitrons: offering new roles to retained introns-the novel regulators of protein diversity and utility.AoB PLANTS · 2024Review
- Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing.Genome biology · 2024Article
- Regulation of alternative splicing and polyadenylation in neurons.Life science alliance · 2023Review
- Article
- Uncovering the impacts of alternative splicing on the proteome with current omics techniques.Wiley interdisciplinary reviews. RNA · 2022Review
- Exonic splicing code and protein binding sites for calcium.Nucleic acids research · 2022Article
125 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Splicing of short introns by the nuclear pre-mRNA splicing machinery is thought to proceed via an "intron definition" mechanism, in which the 5' and 3' splice sites (5'ss, 3'ss, respectively) are initially recognized and paired across the intron. Here, we describe a computational analysis of sequence features involved in recognition of short introns by using available transcript data from five eukaryotes with complete or nearly complete genomic sequences. The information content of five different transcript features was measured by using methods from information theory, and Monte Carlo simulations were used to determine the amount of information required for accurate recognition of short introns in each organism. We conclude: (i) that short introns in Drosophila melanogaster and Caenorhabditis elegans contain essentially all of the information for their recognition by the splicing machinery, and computer programs that simulate splicing specificity can predict the exact boundaries of approximately 95% of short introns in both organisms; (ii) that in yeast, the 5'ss, branch signal, and 3'ss can accurately identify intron locations but do not precisely determine the location of 3' cleavage in every intron; and (iii) that the 5'ss, branch signal, and 3'ss are not sufficient to accurately identify short introns in plant and human transcripts, but that specific subsets of candidate intronic enhancer motifs can be identified in both human and Arabidopsis that contribute dramatically to the accuracy of splicing simulators.
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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.