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Updated: Jun 23, 2026
08:35
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
Comparative component analysis of exons with different splicing frequencies.
Shiqin Song1, Qianli Huang, Jiaming Guo
1Department of Chemistry, University of Science and Technology of China, Hefei, China.
Plos One
|May 1, 2009
Summary
Splicing frequency influences exon characteristics. Lower frequency exons are longer, have higher GC content, and may be newly evolved, originating from repetitive sequences with altered splicing sites.
Area of Science:
- Molecular Biology
- Genomics
- Evolutionary Biology
Background:
- Transcriptional isoforms arise from differential exon splicing.
- Understanding the regulation and evolution of alternatively spliced exons (ASEs) is crucial.
Purpose of the Study:
- To classify exons based on splicing frequency.
- To investigate the compositional and regulatory properties of exons with varying splicing frequencies.
- To explore the evolutionary origins of exons with different splicing patterns.
Main Methods:
- Classification of exons from human and mouse orthologous genes into four types based on splicing frequency.
- Analysis of exon length, GC content, and presence of splicing and repetitive elements.
- Comparative analysis of alternatively spliced human genes and non-alternatively spliced (NAS) mouse orthologs.
Main Results:
- Exons with lower splicing frequencies exhibit greater lengths, higher GC content, and increased presence of splicing and repetitive elements.
- Splicing frequency appears to be influenced by exon composition and regulatory elements.
- Exons with lower splicing frequencies in humans may represent newly evolved exons in mouse orthologs, potentially originating from repetitive sequences with altered splicing sites.
Conclusions:
- Splicing frequency is a critical factor influencing exon properties and regulation.
- Exon evolution may involve changes in splicing frequency, leading to novel functions.
- Repetitive sequences and mutations in splicing sites could contribute to the origin of alternatively spliced exons.
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