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

Masaru Tomita, Nobuyoshi Shimizu, Douglas L. Brutlag

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

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 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 languageEnglish
Pages (from-to)1219-1223
Number of pages5
JournalMolecular Biology and Evolution
Volume13
Issue number9
Publication statusPublished - 1996 Nov

Fingerprint

Reading Frames
codons
Codon
Introns
introns
Exons
exons
eukaryote
primate
rodent
Mammals
vertebrate
mammal
invertebrate
Nucleic Acid Databases
Invertebrates
Eukaryota
Primates
eukaryotic cells
Vertebrates

Keywords

  • exon
  • intron
  • sequence analysis
  • splicing

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

Introns and reading frames : Correlation between splicing sites and their codon positions. / Tomita, Masaru; Shimizu, Nobuyoshi; Brutlag, Douglas L.

In: Molecular Biology and Evolution, Vol. 13, No. 9, 11.1996, p. 1219-1223.

Research output: Contribution to journalArticle

Tomita, Masaru ; Shimizu, Nobuyoshi ; Brutlag, Douglas L. / Introns and reading frames : Correlation between splicing sites and their codon positions. In: Molecular Biology and Evolution. 1996 ; Vol. 13, No. 9. pp. 1219-1223.
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