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Table 1 Statistics describing the base composition of ORF2 in nLTR-RT

From: Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons

CladesOrganismsN%AT%GC%AGC1GC2GC3PolyANcCAIeCAIRCDIeRCDI
L1Mammals1462.3 ± 1.337.7 ± 1.341.5 ± 1.639.5 ± 1.232.9 ± 1.040.7 ± 2.213.5 ± 3.545.30.740.771.411.54
 Lizard1266.8 ± 1.133.2 ± 1.142.9 ± 1.637.2 ± 1.429.4 ± 0.833.2 ± 2.423.0 ± 6.544.80.720.751.651.71
 Frog3556.4 ± 3.143.6 ± 3.133.4 ± 3.047.4 ± 3.338.3 ± 2.242.8 ± 4.56.3 ± 3.550.90.790.841.251.31
 Fish1863.7 ± 2.136.3 ± 2.133.2 ± 3.439.6 ± 2.430.6 ± 2.232.1 ± 2.811.7 ± 7.443.10.720.751.711.92
Tx1frog257.7 ± 9.042.3 ± 9.028.8 ± 5.348.0 ± 9.235.7 ± 7.243.1 ± 10.66.0 ± 5.750.30.840.841.201.38
 fish1161.4 ± 9.638.6 ± 9.633.1 ± 7.844.6 ± 7.333.7 ± 6.637.5 ± 15.59.7 ± 7.646.10.710.731.551.71
CR1Lizard153.846.233.850.237.850.72.052.40.780.781.151.38
 Frog358.2 ± 1.041.8 ± 1.030.4 ± 0.046.1 ± 1.336.0 ± 1.342.6 ± 0.65.0 ± 1.050.10.850.851.171.86
DaphneFish466.8 ± 3.033.2 ± 3.039.1 ± 1.436.9 ± 2.628.9 ± 2.233.8 ± 4.710.0 ± 2.946.80.610.641.702.00
CrackFish464.7 ± 4.035.3 ± 4.033.6 ± 1.739.3 ± 2.235.3 ± 4.331.3 ± 5.97.0 ± 2.946.50.670.681.702.00
L2Lizard1745.1 ± 1.254.9 ± 1.220.5 ± 1.259.1 ± 1.046.1 ± 0.859.4 ± 2.90.9 ± 0.754.70.770.781.111.37
 Frog252.0 ± 0.948.0 ± 0.921.5 ± 2.049.7 ± 0.846.1 ± 0.248.4 ± 1.62.5 ± 0.749.90.790.811.311.44
 Fish1957.7 ± 4.442.3 ± 4.426.8 ± 3.745.6 ± 3.838.5 ± 4.040.4 ± 6.63.1 ± 2.751.70.740.771.311.49
Rex1Frog351.1 ± 1.248.9 ± 1.227.1 ± 0.548.7 ± 1.643.6 ± 0.555.0 ± 1.41.3 ± 0.654.60.840.831.091.93
 Fish1247.7 ± 4.952.3 ± 4.925.9 ± 2.747.6 ± 2.942.5 ± 2.847.7 ± 10.11.7 ± 2.852.60.770.791.191.48
ILizard154.643.431.950.242.343.7453.20.760.761.201.48
 Fish665.7 ± 1.534.3 ± 1.539.2 ± 2.241.0 ± 1.633.4 ± 0.828.4 ± 2.715.8 ± 6.242.40.720.741.671.80
R4Lizard157.343.738.247.534.346.4251.10.790.771.171.44
 Fish147.552.531.651.343.263.1149.50.700.731.271.40
RTELizard150.050.031.254.341.254.5053.30.790.791.121.36
 Fish545.4 ± 6.154.6 ± 6.123.7 ± 5.357.1 ± 5.346.4 ± 6.460.4 ± 7.30.4 ± 0.550.70.720.741.271.45
PenelopeLizard762.7 ± 3.437.3 ± 3.435.5 ± 1.140.5 ± 4.034.8 ± 0.936.5 ± 5.75.4 ± 2.649.00.750.751.401.61
 Frog1156.4 ± 2.943.4 ± 2.930.2 ± 2.546.0 ± 2.039.7 ± 2.344.1 ± 5.01.5 ± 1.352.70.840.841.151.39
 Fish355.2 ± 1.544.8 ± 1.531.7 ± 1.046.4 ± 3.737.1 ± 1.050.7 ± 0.25.0 ± 5.054.10.680.691.241.62
  1. N = number of consensus sequences; %AT, %GC and %A = % of nucleotides on the positive strand;GC1, GC2 and GC3 = % of GC at the 1st, 2nd and 3rd positions of codons; polyA Average number of potential poly-adenylation signals; Nc = effective number of codons; CAI Codon Adaptation Index, eCAI Exepected CAI, RCDI Realtive Codon Deoptimization Index, eRCDI Expected RCDI