ArticlePLoS computational biology2007
The emergence of alternative 3' and 5' splice site exons from constitutive exons.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 90 citations in OpenAlex.
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- Intronic RNA secondary structural information captured for the humanNAR genomics and bioinformatics · 2024Article
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- Alternative splicing ofbioRxiv : the preprint server for biology · 2024Article
- Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies.Frontiers in immunology · 2024Review
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- Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases.Genes · 2023Review
- Distinct regulatory functions and biological roles of lncRNA splice variants.Molecular therapy. Nucleic acids · 2023Review
- Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog.BMC genomics · 2022Article
- What's in a Gene? The Outstanding Diversity ofCells · 2022Review
- Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes.Advances in drug and alcohol research · 2022Article
- Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing.International journal of molecular sciences · 2021Review
- What's Wrong in a Jump? Prediction and Validation of Splice Site Variants.Methods and protocols · 2021Review
- Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law.Immunogenetics · 2021Article
- A machine learning-based framework for modeling transcription elongation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Computational Methods for Predicting Functions at the mRNA Isoform Level.International journal of molecular sciences · 2020Review
- Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes.International journal of molecular sciences · 2019Review
- Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative 3' and 5' splice site (ss) events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases. However, only few of the characteristics that distinguish these events from alternative cassette exons are known currently. In this study, we compared the characteristics of constitutive exons, alternative cassette exons, and alternative 3'ss and 5'ss exons. The results revealed that alternative 3'ss and 5'ss exons are an intermediate state between constitutive and alternative cassette exons, where the constitutive side resembles constitutive exons, and the alternative side resembles alternative cassette exons. The results also show that alternative 3'ss and 5'ss exons exhibit low levels of symmetry (frame-preserving), similar to constitutive exons, whereas the sequence between the two alternative splice sites shows high symmetry levels, similar to alternative cassette exons. In addition, flanking intronic conservation analysis revealed that exons whose alternative splice sites are at least nine nucleotides apart show a high conservation level, indicating intronic participation in the regulation of their splicing, whereas exons whose alternative splice sites are fewer than nine nucleotides apart show a low conservation level. Further examination of these exons, spanning seven vertebrate species, suggests an evolutionary model in which the alternative state is a derivative of an ancestral constitutive exon, where a mutation inside the exon or along the flanking intron resulted in the creation of a new splice site that competes with the original one, leading to alternative splice site selection. This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution.
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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.