ArticleNucleic acids research2009
Accurate prediction of NAGNAG alternative splicing.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites.Cellular and molecular life sciences : CMLS · 2021Article
- An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.PLoS computational biology · 2021Article
- Impact of acceptor splice site NAGTAG motif on exon recognition.Molecular biology reports · 2019Article
- Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans.Genome research · 2015Article
- Article
- Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome.Human molecular genetics · 2015Article
- Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons.Nucleic acids research · 2014Article
- Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes.BMC genomics · 2014Article
- Article
- Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.BioMed research international · 2014Article
- Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome?Genome biology · 2012Article
- Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.PLoS biology · 2012Article
- Strict 3' splice site sequence requirements for U2 snRNP recruitment after U2AF binding underlie a genetic defect leading to autoimmune disease.RNA (New York, N.Y.) · 2011Article
- The Drosophila melanogaster transcriptome by paired-end RNA sequencing.Genome research · 2011Article
- Alternative splicing at a NAGNAG acceptor site as a novel phenotype modifier.PLoS genetics · 2010Article
- 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
- Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens.BMC plant biology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing (AS) involving NAGNAG tandem acceptors is an evolutionarily widespread class of AS. Recent predictions of alternative acceptor usage reported better results for acceptors separated by larger distances, than for NAGNAGs. To improve the latter, we aimed at the use of Bayesian networks (BN), and extensive experimental validation of the predictions. Using carefully constructed training and test datasets, a balanced sensitivity and specificity of >or=92% was achieved. A BN trained on the combined dataset was then used to make predictions, and 81% (38/47) of the experimentally tested predictions were verified. Using a BN learned on human data on six other genomes, we show that while the performance for the vertebrate genomes matches that achieved on human data, there is a slight drop for Drosophila and worm. Lastly, using the prediction accuracy according to experimental validation, we estimate the number of yet undiscovered alternative NAGNAGs. State of the art classifiers can produce highly accurate prediction of AS at NAGNAGs, indicating that we have identified the major features of the 'NAGNAG-splicing code' within the splice site and its immediate neighborhood. Our results suggest that the mechanism behind NAGNAG AS is simple, stochastic, and conserved among vertebrates and beyond.
Indexed as
Identifiers
What OpenQuestion holds
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.