@Article{Hiller:Huse:Platzer:Creat_and_disru:2005,
  author =	 {Hiller, Michael and Huse, Klaus and Platzer, Matthias and 
                  Backofen, Rolf},
  title =	 {Creation and disruption of protein features by alternative 
                  splicing -- a novel mechanism to modulate function},
  journal =	 {Genome Biol},
  year =	 {2005},
  issn  =        {1465-6914},
  issn  =        {1465-6906},
  volume =	 {6},
  number =	 {7},
  pages =	 {R58},
  user =	 {hiller},
  publists =	 {All and Michael Hiller and Rolf Backofen},
  pmid =	 {15998447},
  abstract =	 {BACKGROUND: Alternative splicing often occurs in the coding 
                  sequence and alters protein structure and function. It is 
                  mainly carried out in two ways: by skipping exons that 
                  encode a certain protein feature and by introducing a 
                  frameshift that changes the downstream protein sequence. 
                  These mechanisms are widespread and well investigated. 
                  RESULTS: Here, we propose an additional mechanism of 
                  alternative splicing to modulate protein function. This 
                  mechanism creates a protein feature by putting together two 
                  non-consecutive exons or destroys a feature by inserting an 
                  exon in its body. In contrast to other mechanisms, the 
                  individual parts of the feature are present in both splice 
                  variants but the feature is only functional in the splice 
                  form where both parts are merged. We provide evidence for 
                  this mechanism by performing a genome-wide search with four 
                  protein features: transmembrane helices, phosphorylation and 
                  glycosylation sites, and Pfam domains. CONCLUSION: We 
                  describe a novel type of event that creates or removes a 
                  protein feature by alternative splicing. Current data 
                  suggest that these events are rare. Besides the four 
                  features investigated here, this mechanism is conceivable 
                  for many other protein features, especially for small linear 
                  protein motifs. It is important for the characterization of 
                  functional differences of two splice forms and should be 
                  considered in genome-wide annotation efforts. Furthermore, 
                  it offers a novel strategy for ab initio prediction of 
                  alternative splice events.}
}