@Article{Sinha:Zimmer:Bolte:Ident_and_chara:2010,
  author =	 {Sinha, Rileen and Zimmer, Andreas D. and Bolte, Kathrin and 
                  Lang, Daniel and Reski, Ralf and Platzer, Matthias and 
                  Rensing, Stefan A. and Backofen, Rolf},
  title =	 {Identification and characterization of {NAGNAG} alternative 
                  splicing in the moss {Physcomitrella} patens},
  issn  =        {1471-2229},
  journal =	 {BMC Plant Biol},
  year =	 2010,
  volume =	 10,
  pages =	 76,
  user =	 {kousik},
  pmid =	 20426810,
  doi = 	 {10.1186/1471-2229-10-76},
  abstract =	 {BACKGROUND: Alternative splicing (AS) involving tandem 
                  acceptors that are separated by three nucleotides (NAGNAG) 
                  is an evolutionarily widespread class of AS, which is well 
                  studied in Homo sapiens (human) and Mus musculus (mouse). It 
                  has also been shown to be common in the model seed plants 
                  Arabidopsis thaliana and Oryza sativa (rice). In one of the 
                  first studies involving sequence-based prediction of AS in 
                  plants, we performed a genome-wide identification and 
                  characterization of NAGNAG AS in the model plant 
                  Physcomitrella patens, a moss. RESULTS: Using Sanger data, 
                  we found 295 alternatively used NAGNAG acceptors in P. 
                  patens. Using 31 features and training and test datasets of 
                  constitutive and alternative NAGNAGs, we trained a 
                  classifier to predict the splicing outcome at NAGNAG tandem 
                  splice sites (alternative splicing, constitutive at the 
                  first acceptor, or constitutive at the second acceptor). Our 
                  classifier achieved a balanced specificity and sensitivity 
                  of >or= 89%. Subsequently, a classifier trained exclusively 
                  on data well supported by transcript evidence was used to 
                  make genome-wide predictions of NAGNAG splicing outcomes. By 
                  generation of more transcript evidence from a 
                  next-generation sequencing platform (Roche 454), we found 
                  additional evidence for NAGNAG AS, with altogether 664 
                  alternative NAGNAGs being detected in P. patens using all 
                  currently available transcript evidence. The 454 data also 
                  enabled us to validate the predictions of the classifier, 
                  with 64% (80/125) of the well-supported cases of AS being 
                  predicted correctly. CONCLUSION: NAGNAG AS is just as common 
                  in the moss P. patens as it is in the seed plants A. 
                  thaliana and O. sativa (but not conserved on the level of 
                  orthologous introns), and can be predicted with high 
                  accuracy. The most informative features are the nucleotides 
                  in the NAGNAG and in its immediate vicinity, along with the 
                  splice sites scores, as found earlier for NAGNAG AS in 
                  animals. Our results suggest that the mechanism behind 
                  NAGNAG AS in plants is similar to that in animals and is 
                  largely dependent on the splice site and its immediate 
                  neighborhood.}
}