ArticleRNA (New York, N.Y.)2004
A computational and experimental approach toward a priori identification of alternatively spliced exons.
Article in RNA (New York, N.Y.), 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed, 48 citations in OpenAlex.
- Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons.BMC genomics · 2017Article
- Article
- Improved identification of conserved cassette exons using Bayesian networks.BMC bioinformatics · 2008Article
- A DNA damage signal activates and derepresses exon inclusion in Drosophila TAF1 alternative splicing.RNA (New York, N.Y.) · 2008Article
- Comparative analysis of sequence features involved in the recognition of tandem splice sites.BMC genomics · 2008Article
- Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.BMC genomics · 2008Article
- Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.PLoS computational biology · 2008Review
- Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation.BMC evolutionary biology · 2007Article
- Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site.RNA (New York, N.Y.) · 2006Article
- A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.Algorithms for molecular biology : AMB · 2006Article
- Article
- Differentiated evolutionary rates in alternative exons and the implications for splicing regulation.BMC evolutionary biology · 2006Article
- The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test.BMC bioinformatics · 2006Article
- Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.BMC bioinformatics · 2006Article
- Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression.Genes & development · 2006Article
- A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones.Genome biology · 2006Article
- Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers.Journal of molecular evolution · 2006Article
- Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse.RNA (New York, N.Y.) · 2005Article
- Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Alternative splicing is a powerful means of regulating gene expression and enhancing protein diversity. In fact, the majority of metazoan genes encode pre-mRNAs that are alternatively spliced to produce anywhere from two to tens of thousands of mRNA isoforms. Thus, an important part of determining the complete proteome of an organism is developing a catalog of all mRNA isoforms. Alternatively spliced exons are typically identified by aligning EST clusters to reference mRNAs or genomic DNA. However, this approach is not useful for genomes that lack robust EST coverage, and tools that enable accurate prediction of alternatively spliced exons would be extraordinarily useful. Here, we use comparative genomics to identify, and experimentally verify, potential alternative exons based solely on their high degree of conservation between Drosophila melanogaster and D. pseudoobscura. At least 40% of the exons that fit our prediction criteria are in fact alternatively spliced. Thus, comparative genomics can be used to accurately predict certain classes of alternative exons without relying on EST data.
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Registered trials
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.