ArticleBMC plant biology2010
Prevalence of alternative splicing choices in Arabidopsis thaliana.
Article in BMC plant biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.
- Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.Plant physiology · 2013Pooled it
- Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Multilayered regulation of iron homeostasis in Arabidopsis.Frontiers in plant science · 2023Review
- Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species.International journal of molecular sciences · 2022Article
- Anno genominis XX: 20 years of Arabidopsis genomics.The Plant cell · 2021Review
- Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing.Plant direct · 2019Article
- Identification and characterization of evolutionarily conserved alternative splicing events in a mangrove genus Sonneratia.Scientific reports · 2018Article
- Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato.International journal of molecular sciences · 2017Article
- ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins.Bioinformatics (Oxford, England) · 2016Article
- Bioinformatics resources for pollen.Plant reproduction · 2016Review
- Enhanced Salt Tolerance Conferred by the Complete 2.3 kb cDNA of the Rice Vacuolar Na(+)/H(+) Antiporter Gene Compared to 1.9 kb Coding Region with 5' UTR in Transgenic Lines of Rice.Frontiers in plant science · 2016Article
- Identification of alternative splicing events by RNA sequencing in early growth tomato fruits.BMC genomics · 2015Article
- Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR.PeerJ · 2015Article
- Article
- Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes.BMC genomics · 2014Article
- 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
- A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Complexity of the alternative splicing landscape in plants.The Plant cell · 2013Review
- RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing.Plant physiology · 2013Article
- Genome-wide landscape of alternative splicing events in Brachypodium distachyon.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
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
backgroundAround 14% of protein-coding genes of Arabidopsis thaliana genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced genes in Arabidopsis, the relative expression level of individual splicing variants is unknown.
resultsWe investigated prevalence of alternative splicing (AS) events in Arabidopsis thaliana using ESTs. We found that for most AS events with ample EST coverage, the majority of overlapping ESTs strongly supported one major splicing choice, with less than 10% of ESTs supporting the minor form. Analysis of ESTs also revealed a small but noteworthy subset of genes for which alternative choices appeared with about equal prevalence, suggesting that for these genes the variant splicing forms co-occur in the same cell types. Of the AS events in which both forms were about equally prevalent, more than 80% affected untranslated regions or involved small changes to the encoded protein sequence.
conclusionsCurrently available evidence from ESTs indicates that alternative splicing in Arabidopsis occurs and affects many genes, but for most genes with documented alternative splicing, one AS choice predominates. To aid investigation of the role AS may play in modulating function of Arabidopsis genes, we provide an on-line resource (ArabiTag) that supports searching AS events by gene, by EST library keyword search, and by relative prevalence of minor and major forms.
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