title: Phylogenetically widespread alternative splicing at unusual GYNGYN donors.
abstract: BACKGROUND
  Splice donor sites have a highly conserved GT or GC dinucleotide and an extended intronic consensus sequence GTRAGT that reflects the sequence complementarity to the U1 snRNA. Here, we focus on unusual donor sites with the motif GYNGYN (Y stands for C or T; N stands for A, C, G, or T).
  
  
  RESULTS
  While only one GY functions as a splice donor for the majority of these splice sites in human, we provide computational and experimental evidence that 110 (1.3%) allow alternative splicing at both GY donors. The resulting splice forms differ in only three nucleotides, which results mostly in the insertion/deletion of one amino acid. However, we also report the insertion of a stop codon in four cases. Investigating what distinguishes alternatively from not alternatively spliced GYNGYN donors, we found differences in the binding to U1 snRNA, a strong correlation between U1 snRNA binding strength and the preferred donor, over-represented sequence motifs in the adjacent introns, and a higher conservation of the exonic and intronic flanks between human and mouse. Extending our genome-wide analysis to seven other eukaryotic species, we found alternatively spliced GYNGYN donors in all species from mouse to Caenorhabditis elegans and even in Arabidopsis thaliana. Experimental verification of a conserved GTAGTT donor of the STAT3 gene in human and mouse reveals a remarkably similar ratio of alternatively spliced transcripts in both species.
  
  
  CONCLUSIONS
  In contrast to alternative splicing in general, GYNGYN donors in addition to NAGNAG acceptors enable subtle protein variations.
authors.affiliation: Institute of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany. hiller@informatik.uni-freiburg.de
authors.forename: Michael
authors.initials: M
authors.lastname: Hiller
authors.forename: Klaus
authors.initials: K
authors.lastname: Huse
authors.forename: Karol
authors.initials: K
authors.lastname: Szafranski
authors.forename: Philip
authors.initials: P
authors.lastname: Rosenstiel
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D018388:Codon, Terminator; D005091:Exons; D006801:Humans; D007438:Introns; D051379:Mice; D010802:Phylogeny; D012342:RNA, Small Nuclear / Q000378:metabolism; D050796:STAT3 Transcription Factor / Q000235:genetics
chemical_list: D018388:Codon, Terminator; D012342:RNA, Small Nuclear; D050796:STAT3 Transcription Factor; C405483:U1 small nuclear RNA