BIOINFORMATICS<-->STRUCTURE
Jerusalem, Israel, November 17-21, 1996

Abstract


Introns and reading frames: correlation between splicing sites and their codon positions

Masaru Tomita(1), Nobuyoshi Shimizu(2) and Doug Brutlag(3)

(1)Department of Environmental Information and Department of Molecular Biology Keio University, 5322 Endo, Fujisawa, 252, JAPAN
(2)Department of Molecular Biology, Keio University
(3)Department of Biochemistry, Stanford University

mt@sfc.keio.ac.jp


Computer analyses of the entire Genbank database were conducted to examine correlation between splicing sites and codon positions in reading frames. Intron insertion patterns (i.e., splicing site locations with respect to codon positions) have been analyzed for all of the 64 codons of all the eukaryote taxonomical groups: primates, rodents, mammals, vertebrates, invertebrates and plants.
We found that reading frames are interrupted by an intron at a codon boundary (as oppose to the middle of a codon) significantly more often than expected. This observation is consistent with the {\it exon shuffling hypothesis}, because exons that end at codon boundaries can be concatenated without causing a frame shift and thus are evolutionarily advantageous.
On the other hand, when introns interrupt at the middle of codons, they exist in between the first and second bases much more frequently than the second and third bases, despite the fact that boundaries between the first and second bases of codons are generally far more important than those between the second and third bases. The reason is not clear and yet to be explained.
We also show that the length of an exon is a multiple of 3 more frequently than expected. Furthermore, the total length of two consecutive exons is also more frequently a multiple of 3.
All the observations above are consistent with the recently published results by Long, Rosenberg and Gilbert (1995).


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