ArticleNucleic acids research2014
Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 2 of them syntheses that pooled it.
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Who cites it
12 citing papers in PubMed, 2 syntheses or guidelines pooled it, 25 citations in OpenAlex.
- Decoding the role of aberrant RNA alternative splicing in hepatocellular carcinoma: a comprehensive review.Journal of cancer research and clinical oncology · 2023Pooled it
- Quantitative RNA-seq meta-analysis of alternative exon usage inGenome research · 2017Pooled it
- Splicing accuracy varies across human introns, tissues, age and disease.Nature communications · 2025Article
- In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue.PLoS genetics · 2022Article
- An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.PLoS computational biology · 2021Article
- Systematic evaluation of isoform function in literature reports of alternative splicing.BMC genomics · 2018Article
- Article
- Alternative mRNA processing sites decrease genetic variability while increasing functional diversity.Transcription · 2018Review
- The fitness cost of mis-splicing is the main determinant of alternative splicing patterns.Genome biology · 2017Article
- Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts.Journal of visualized experiments : JoVE · 2016Article
- Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Non-coding RNA: what is functional and what is junk?Frontiers in genetics · 2015Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this issue, we studied the most common form of alternative 5' splice sites-GYNNGYs (Y = C/T), where both GYs can function as splice sites. Global analyses suggest that splicing noise (due to stochasticity of splicing process) can cause AS at GYNNGYs, evidenced by higher AS frequency in non-coding than in coding regions, in non-conserved than in conserved genes and in lowly expressed than in highly expressed genes. However, ∼20% AS GYNNGYs in humans and ∼3% in mice exhibit tissue-dependent regulation. Consistent with being functional, regulated GYNNGYs are more conserved than unregulated ones. And regulated GYNNGYs have distinctive sequence features which may confer regulation. Particularly, each regulated GYNNGY comprises two splice sites more resembling each other than unregulated GYNNGYs, and has more conserved downstream flanking intron. Intriguingly, most regulated GYNNGYs may tune gene expression through coupling with nonsense-mediated mRNA decay, rather than encode different proteins. In summary, AS at GYNNGY 5' splice sites is primarily splicing noise, and secondarily a way of regulation.
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Registered trials
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