TABLE 1

Difference in codon usage (ΔRSCU) between highly and poorly expressed genes in three different tissues

SpleenLiverTestis
AllGC richGC poorAllGC richGC poorAllGC richGC poor
AsnAACa0.37++0.28+0.36++0.32++0.27+0.38++0.090.030.16
AAT−0.37−0.28−0.36−0.32−0.27−0.38−0.09−0.03−0.16
AspGAC0.36++0.35++0.31++0.30++0.27+0.28+0.04−0.020.09
GAT−0.36−0.35−0.31−0.30−0.27−0.28−0.040.02−0.09
CysTGC0.35++0.29+0.30++0.27+0.20+0.27+0.060.000.04
TGT−0.35−0.29−0.30−0.27−0.18−0.27−0.060.00−0.04
GlnCAA−0.33−0.28−0.33−0.28−0.28−0.26−0.13−0.10−0.11
CAG0.33++0.28+0.33++0.28+0.28+0.26+0.130.100.11
GluGAA−0.49−0.44−0.46−0.40−0.38−0.41−0.14−0.05−0.19
GAG0.49++0.44++0.46++0.40++0.38++0.41++0.140.050.19
HisCAC0.41++0.41++0.36++0.32++0.32++0.34++0.090.070.07
CAT−0.41−0.41−0.36−0.32−0.32−0.34−0.09−0.07−0.07
LysAAA−0.45−0.41−0.43−0.36−0.33−0.43−0.14−0.09−0.15
AAG0.45++0.41++0.43++0.36++0.33++0.43++0.140.090.15
PheTTC0.43++0.39++0.41++0.37++0.34++0.40++0.120.060.13
TTT−0.43−0.39−0.41−0.37−0.34−0.40−0.12−0.06−0.13
TyrTAC0.38++0.31++0.35++0.31++0.26+0.33++0.100.050.17
TAT−0.38−0.31−0.35−0.31−0.26−0.33−0.10−0.05−0.17
IleATA−0.35−0.20−0.20−0.32−0.19−0.24−0.11−0.04−0.06
ATC0.79++0.47++0.49++0.67++0.40++0.48++0.180.020.16
ATT−0.44−0.26−0.29−0.35−0.21−0.24−0.070.01−0.10
AlaGCA−0.49−0.21−0.24−0.37−0.16−0.21−0.16−0.04−0.09
GCC0.61++0.23+0.29+0.51++0.21+0.27+0.140.020.09
GCG0.140.080.070.100.030.050.02−0.010.04
GCT−0.26−0.10−0.12−0.24−0.08−0.120.000.03−0.04
GlyGGA−0.59−0.25−0.29−0.46−0.20−0.26−0.21−0.12−0.11
GGC0.51++0.23+0.22+0.45++0.22+0.22+0.140.040.12
GGG0.26+0.110.140.160.060.080.010.00−0.01
GGT−0.18−0.08−0.07−0.15−0.08−0.050.070.080.00
ProCCA−0.39−0.16−0.18−0.35−0.19−0.14−0.11−0.07−0.08
CCC0.56++0.23+0.25+0.48++0.22+0.26+0.120.050.09
CCG0.170.080.080.140.070.050.030.000.05
CCT−0.34−0.15−0.15−0.27−0.11−0.16−0.050.02−0.06
ThrACA−0.42−0.18−0.20−0.40−0.17−0.22−0.12−0.04−0.08
ACC0.59++0.33++0.29+0.53++0.28+0.33++0.190.060.10
ACG0.190.070.060.180.080.050.030.010.05
ACT−0.36−0.23−0.15−0.31−0.18−0.16−0.10−0.03−0.08
ValGTA−0.37−0.17−0.18−0.32−0.15−0.18−0.08−0.02−0.04
GTC0.24+0.120.110.180.090.090.030.000.02
GTG0.62++0.26+0.30++0.51++0.24+0.26+0.150.010.09
GTT−0.50−0.21−0.23−0.38−0.17−0.17−0.100.01−0.06
ArgAGA−1.00−0.29−0.31−0.84−0.26−0.28−0.33−0.07−0.11
AGG−0.22−0.07−0.07−0.18−0.05−0.10−0.160.01−0.11
CGA−0.17−0.06−0.05−0.13−0.05−0.02−0.04−0.02−0.02
CGC0.75++0.21+0.24+0.66++0.23+0.25+0.27+0.050.13
CGG0.67++0.21+0.20+0.47++0.180.130.180.010.10
CGT−0.030.00−0.010.030.020.030.080.020.00
LeuTTA−0.51−0.14−0.16−0.44−0.14−0.15−0.16−0.05−0.04
TTG−0.33−0.11−0.11−0.25−0.08−0.11−0.030.01−0.03
CTA−0.19−0.06−0.05−0.20−0.07−0.05−0.08−0.02−0.03
CTC0.34++0.090.090.28+0.080.090.06−0.010.01
CTG1.16++0.34++0.36++0.96++0.31++0.35++0.31++0.040.13
CTT−0.46−0.12−0.13−0.35−0.10−0.12−0.090.02−0.05
SerAGC0.50++0.150.140.43++0.130.150.04−0.010.05
AGT−0.37−0.13−0.11−0.34−0.11−0.11−0.120.00−0.06
TCA−0.38−0.08−0.13−0.36−0.09−0.14−0.10−0.03−0.04
TCC0.44++0.140.140.41++0.130.150.170.030.08
TCG0.110.030.030.110.030.040.060.010.01
TCT−0.30−0.10−0.08−0.25−0.08−0.10−0.050.00−0.04
  • a Optimal codons (in underlined italic) defined by a positive ΔRSCU (>0.2) in both GC-rich and GC-poor isochores in tissues with no detectable TAMB (liver and spleen). ++, ΔRSCU > 0.3; +, ΔRSCU > 0.2.