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Indeed, both in twofold- and fourfold-degenerate codon families, the T-ending codons are greatly favored in most synonymous codons, whereas C-ending codons are evidently avoided.
This is because the small effective population sizes (Ne < 10) of most mammal species mean that the effect of genetic drift is likely to overwhelm the small selection coefficients that distinguish most synonymous codons (1/ 2Ne) > s) [ 4, 15].
For example, amino acids (Arg, Leu, or Ile) with a relatively low GCsyn in each group also have the most synonymous codons within that group, some of which are the least used codons.
Because most synonymous codons differ at only the third nucleotide positions, guanine and cytosine content at the third codon position (GC3) is a good indicator of the extent of SCUB.
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It is well established that in most organisms synonymous codons are not randomly used [ 36, 37].
Bold values indicate the most frequent synonymous codons for each amino acid and species, italic values indicate rare codons.
'Georgia Belle' exhibited AAG (Lysine) to AAA (Lysine) as the most common synonymous codon change (306 events), and GGA (Glycine) to AAA (Lysine) as the most common non-synonymous change with 282 events.
'Dr. Davis' exhibited GGA (Glycine) to AAA (Lysine) as the most common non-synonymous codon change, with 183 events, and AAC (Asparagine) to AAT (Asparagine) as the most common synonymous codon change with 176 events.
The wobble site of the anticodon of the 22 mitochondrial tRNAs is either U or G to pair with the most abundant synonymous codon, with only one exception.
Only in two amino acids (Phe and Trp) the most frequent synonymous codon ended in A or T (and these are the termination codons).
The relative adaptiveness values of each codon are defined as ratio of occurrences of the codon to occurrences of the most abundant synonymous codon, using the ribosomal gene sequences from each species.
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