Molecular Biology and Evolution, Vol 13, 1219-1223, Copyright © 1996 by Society for Molecular Biology and Evolution
M Tomita, N Shimizu and DL Brutlag
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 74 codons of all the
eukaryote taxonomic groups: primates, rodents mammals, vertebrates,
invertebrates, and plants. We found that reading frames are interrupted by
an intron at a codon boundary (as opposed to the middle of a codon)
significantly more often than expected. This observation is consistent with
the 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 middles of codons, they exist in between the first and second bases
much more frequently than between 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 for this 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
results recently published by Long, Rosenberg, and Gilbert (1995).
ORIGINAL ARTICLE
Introns and reading frames: correlation between splicing sites and their codon positions
Department of Environmental Information, Keio University, Japan. mt@sfc.keio.ac.jp
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. Kamhi, G. Yahalom, G. Kass, Y. Hacham, R. Sperling, and J. Sperling AUG sequences are required to sustain nonsense-codon-mediated suppression of splicing Nucleic Acids Res., July 19, 2006; 34(12): 3421 - 3433. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. D. G. de Roos Origins of introns based on the definition of exon modules and their conserved interfaces Bioinformatics, January 1, 2005; 21(1): 2 - 9. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. ITOH, T. WASHIO, and M. TOMITA Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes RNA, July 1, 2004; 10(7): 1005 - 1018. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Kaessmann, S. Zollner, A. Nekrutenko, and W.-H. Li Signatures of Domain Shuffling in the Human Genome Genome Res., November 1, 2002; 12(11): 1642 - 1650. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Clark and T. A. Thanaraj Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human Hum. Mol. Genet., February 1, 2002; 11(4): 451 - 464. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Long and C. Rosenberg Testing the "Proto-splice Sites" Model of Intron Origin: Evidence from Analysis of Intron Phase Correlations Mol. Biol. Evol., December 1, 2000; 17(12): 1789 - 1796. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Saxonov, I. Daizadeh, A. Fedorov, and W. Gilbert EID: the Exon-Intron Database--an exhaustive database of protein-coding intron-containing genes Nucleic Acids Res., January 1, 2000; 28(1): 185 - 190. [Abstract] [Full Text] [PDF]
|
|