ArticleComparative and functional genomics2011
Factors affecting splicing strength of yeast genes.
Article in Comparative and functional genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Who cites it
9 citing papers in PubMed.
- Mechanism of alternative splicing of yeast HEH1 through competing 5' splice sites.Nature communications · 2025Article
- DecodingbioRxiv : the preprint server for biology · 2025Article
- Splicing factor Prp18p promotes genome-wide fidelity of consensus 3'-splice sites.Nucleic acids research · 2023Article
- The SR-protein Npl3 is an essential component of the meiotic splicing regulatory network in Saccharomyces cerevisiae.Nucleic acids research · 2021Article
- DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution.The Journal of heredity · 2017Article
- Bioinformatics and Drug Discovery.Current topics in medicinal chemistry · 2017Review
- DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.Molecular biology and evolution · 2013Article
- Functional motifs in Escherichia coli NC101.International journal of molecular and cellular medicine · 2013Article
- Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction.Scientifica · 2012Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate and efficient splicing is of crucial importance for highly-transcribed intron-containing genes (ICGs) in rapidly replicating unicellular eukaryotes such as the budding yeast Saccharomyces cerevisiae. We characterize the 5' and 3' splice sites (ss) by position weight matrix scores (PWMSs), which is the highest for the consensus sequence and the lowest for splice sites differing most from the consensus sequence and used PWMS as a proxy for splicing strength. HAC1, which is known to be spliced by a nonspliceosomal mechanism, has the most negative PWMS for both its 5' ss and 3' ss. Several genes under strong splicing regulation and requiring additional splicing factors for their splicing also have small or negative PWMS values. Splicing strength is higher for highly transcribed ICGs than for lowly transcribed ICGs and higher for transcripts that bind strongly to spliceosomes than those that bind weakly. The 3' splice site features a prominent poly-U tract before the 3'AG. Our results suggest the potential of using PWMS as a screening tool for ICGs that are either spliced by a nonspliceosome mechanism or under strong splicing regulation in yeast and other fungal species.
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Registered trials
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