ArticleGenome biology2006
Phylogenetically widespread alternative splicing at unusual GYNGYN donors.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 37 citations in OpenAlex.
- Molecular divergence ofZoological research · 2026Article
- Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs.Nucleic acids research · 2024Article
- Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders.NPJ genomic medicine · 2022Article
- CoSpliceNet: a framework for co-splicing network inference from transcriptomics data.BMC genomics · 2016Article
- Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts.Journal of visualized experiments : JoVE · 2016Article
- Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.Nucleic acids research · 2016Article
- A mix of S and ΔS variants of STAT3 enable survival of activated B-cell-like diffuse large B-cell lymphoma cells in culture.Oncogenesis · 2016Article
- Insight into the role of alternative splicing within the RBM10v1 exon 10 tandem donor site.BMC research notes · 2015Article
- Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells.PloS one · 2015Article
- Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Article
- Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis.F1000Research · 2014Review
- Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence.BMC bioinformatics · 2012Article
- The Drosophila melanogaster transcriptome by paired-end RNA sequencing.Genome research · 2011Article
- Sequence features involved in the mechanism of 3' splice junction wobbling.BMC molecular biology · 2010Article
- TassDB2 - A comprehensive database of subtle alternative splicing events.BMC bioinformatics · 2010Article
- Characterization of conserved tandem donor sites and intronic motifs required for alternative splicing in corticosteroid receptor genes.Endocrinology · 2009Article
- A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.Nucleic acids research · 2008Article
- Assessing the fraction of short-distance tandem splice sites under purifying selection.RNA (New York, N.Y.) · 2008Article
- Selection against tandem splice sites affecting structured protein regions.BMC evolutionary biology · 2008Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSplice donor sites have a highly conserved GT or GC dinucleotide and an extended intronic consensus sequence GTRAGT that reflects the sequence complementarity to the U1 snRNA. Here, we focus on unusual donor sites with the motif GYNGYN (Y stands for C or T; N stands for A, C, G, or T).
resultsWhile only one GY functions as a splice donor for the majority of these splice sites in human, we provide computational and experimental evidence that 110 (1.3%) allow alternative splicing at both GY donors. The resulting splice forms differ in only three nucleotides, which results mostly in the insertion/deletion of one amino acid. However, we also report the insertion of a stop codon in four cases. Investigating what distinguishes alternatively from not alternatively spliced GYNGYN donors, we found differences in the binding to U1 snRNA, a strong correlation between U1 snRNA binding strength and the preferred donor, over-represented sequence motifs in the adjacent introns, and a higher conservation of the exonic and intronic flanks between human and mouse. Extending our genome-wide analysis to seven other eukaryotic species, we found alternatively spliced GYNGYN donors in all species from mouse to Caenorhabditis elegans and even in Arabidopsis thaliana. Experimental verification of a conserved GTAGTT donor of the STAT3 gene in human and mouse reveals a remarkably similar ratio of alternatively spliced transcripts in both species.
conclusionIn contrast to alternative splicing in general, GYNGYN donors in addition to NAGNAG acceptors enable subtle protein variations.
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