A circular code in the protein coding genes of mitochondria.
A new maximal circular code X0(MIT) with two permutated maximal circular codes X1(MIT) and X2(MIT) is identified in the protein coding genes of mitochondria. The three subsets of 20 trinucleotides X0(MIT)={ACA, ACC, ATA, ATC, CTA, CTC, GAA, GAC, GAT, GCA, GCC, GCT, GGA, GGC, GGT, GTA, GTC, GTT, TTA, TTC}, X1(MIT) and X2(MIT) are in frame 0 (reading frame), 1 and 2 respectively. X1(MIT) and X2(MIT) are deduced by one and two circular permutations of X0(MIT) respectively. The code X0(MIT) has four important properties: a length of the minimal window to automatically retrieve frame 0 which is equal to five nucleotides; an occurrence probability equal to 6.3 x 10(-5); a low frequency (12% in average) of misplaced trinucleotides in the shifted frames; and an occurrence of four types of nucleotides in the first and second trinucleotide sites but no nucleotide G in the third trinucleotide site. Several biological consequences are presented in the Discussion.
Arquès
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Equipe de Biologie Théorique, Université de Marne la Vallée, Institut Gaspard Monge, 2 rue de la Butte Verte, 93160 Noisy le Grand, France. arques@univ-mlv.fr
Michel
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CJ
D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D003062:Codon; D004272:DNA, Mitochondrial; D005057:Eukaryotic Cells; D008928:Mitochondria / Q000235:genetics*; D008969:Molecular Sequence Data; D011387:Prokaryotic Cells; D011506:Proteins / Q000235:genetics*; D016364:Reading Frames
D000596:Amino Acids; D003062:Codon; D004272:DNA, Mitochondrial; D011506:Proteins