TABLE 1

Average synonymous base composition in fourfold degenerate codons and codon bias (ENC) compared to base composition in noncoding sequences

nAGCTENC
Coding region
    Short genes (<750 bp)980.1700.2310.4230.17637.82
    Long genes (>4500 bp)480.2260.2420.3330.19949.75
    High recombination (HR)2080.1800.2610.4020.15743.27
    Low recombination (LR)420.2370.2180.3300.21546.41
    HR and short genes330.1520.2530.4460.14935.98
    LR and long genes40.3150.1820.2230.28053.36
Noncoding regiona0.3010.1890.1940.31455.99b

High and low recombination regions are defined as >3 × 10–8/bp/generation and <1 × 10–9/bp/generation, respectively.

  • a Base composition of the nontranscribed strand of long introns (from Moriyama and Hartl 1993).

  • b Expected ENC measure assuming nucleotide frequencies at the third position of codons equivalent to those of the noncoding region and random amino acid usage.