Open Access Highly Accessed Open Badges Research article

Selection against tandem splice sites affecting structured protein regions

Michael Hiller1*, Karol Szafranski2, Klaus Huse2, Rolf Backofen1 and Matthias Platzer2

Author Affiliations

1 Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany

2 Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany

For all author emails, please log on.

BMC Evolutionary Biology 2008, 8:89  doi:10.1186/1471-2148-8-89

Published: 21 March 2008



Alternative selection of splice sites in tandem donors and acceptors is a major mode of alternative splicing. Here, we analyzed whether in-frame tandem sites leading to subtle mRNA insertions/deletions of 3, 6, or 9 nucleotides are under natural selection.


We found multiple lines of evidence that the human protein coding sequences are under selection against such in-frame tandem splice events, indicating that these events are often deleterious. The strength of selection is not homogeneous within the coding sequence as protein regions that fold into a fixed 3D structure (intrinsically ordered) are under stronger selection, especially against sites with a strong minor splice site. Investigating structures of functional protein domains, we found that tandem acceptors are preferentially located at the domain surface and outside structural elements such as helices and sheets. Using three-species comparisons, we estimate that more than half of all mutations that create NAGNAG acceptors in the coding region have been eliminated by selection.


We estimate that ~2,400 introns are under selection against possessing a tandem site.