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Table 1 Analysis of human mitochondrial genes that encode a subunit of complexes I-V of the mitochondrial respiratory chain encoded in the nuclear (a) or mitochondrial (b) genome.

From: E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)

a) Nuclear encoded genes
Complex Gene name Length CAIhm   eCAIhm CAIhm/eCAIhm CAImt   eCAImt CAImt/eCAImt
      p = 0.05 p = 0.05    p = 0.05 p = 0.05
I NDUFS1 2184 0.695 * 0.683 1.018 0.434   0.519 0.836
  NDUFS2 1392 0.765 ** 0.734 1.042 0.391   0.500 0.782
  NDUFS3 795 0.754 * 0.750 1.005 0.402   0.488 0.824
  NDUFS7 642 0.867 ** 0.780 1.112 0.442   0.446 0.991
  NDUFS8 633 0.868 ** 0.796 1.090 0.439   0.465 0.944
  NDUFV1 1395 0.825 ** 0.774 1.066 0.417   0.482 0.865
  NDUFV2 750 0.695   0.703 0.989 0.449   0.519 0.865
II SDHC 510 0.699 * 0.679 1.029 0.377   0.457 0.825
  SDHD 480 0.663 * 0.654 1.014 0.387   0.464 0.834
  SDHA 1995 0.768 * 0.750 1.024 0.423   0.496 0.853
  SDHB 843 0.778 ** 0.754 1.032 0.454   0.481 0.944
III UQCRFS1 825 0.711 * 0.711 1.000 0.391   0.483 0.810
  CYC1 978 0.759 * 0.750 1.012 0.379   0.449 0.844
IV COX10 1332 0.744 ** 0.713 1.043 0.454   0.462 0.983
  COX11 831 0.738 * 0.725 1.018 0.407   0.513 0.793
  COX15 1140 0.707 * 0.688 1.028 0.411   0.472 0.871
V ATP5B 1590 0.714 * 0.698 1.023 0.412   0.507 0.813
  ATP5A1 1512 0.695 * 0.684 1.016 0.409   0.519 0.788
  ATP5C1 897 0.726 * 0.705 1.030 0.463   0.509 0.910
  ATP5O 642 0.700 ** 0.681 1.028 0.429   0.486 0.883
  ATP5D 507 0.807 ** 0.748 1.079 0.410   0.426 0.962
  ATP5G1 411 0.776 ** 0.707 1.098 0.456   0.482 0.946
  ATP5G2 474 0.752 ** 0.686 1.096 0.472 * 0.451 1.047
  ATP5G3 429 0.720 ** 0.678 1.062 0.430   0.510 0.843
  ATP6V1A 1854 0.709 * 0.702 1.010 0.451   0.525 0.859
  ATP6V1B1 1536 0.703   0.711 0.989 0.439   0.514 0.854
  ATP6V1D 744 0.676   0.697 0.970 0.430   0.522 0.824
  ATP6V1E1 681 0.721 * 0.713 1.011 0.431   0.500 0.862
  ATP6V1E2 681 0.777 ** 0.733 1.060 0.410   0.466 0.880
  TCIRG1 2493 0.857 ** 0.781 1.097 0.421   0.434 0.970
  ATP6V0D2 1053 0.732 * 0.722 1.014 0.456   0.518 0.880
  ATP6V0C 468 0.838 ** 0.748 1.120 0.511 ** 0.461 1.108
  ATP6F 618 0.803 ** 0.741 1.084 0.510   0.514 0.992
  ATP6V0D1 1056 0.831 ** 0.793 1.048 0.457   0.495 0.923
  ATP6V0A1 2496 0.758 * 0.734 1.033 0.424   0.507 0.836
  ATP6V0A4 2523 0.770 ** 0.735 1.048 0.458   0.494 0.927
  ATP6V0A2 2571 0.748 * 0.728 1.027 0.450   0.491 0.916
b) Mitochondrial encoded genes
Complex Gene Name Length CAI hm   eCAI hm CAI hm /eCAI hm CAI mt   eCAI mt CAI mt /eCAI mt
      p = 0.05 p = 0.05    p = 0.05 p = 0.05
I ND1 957 0.635   0.796 0.798 0.760 ** 0.456 1.667
  ND2 1044 0.616   0.774 0.796 0.677 ** 0.457 1.481
  ND3 345 0.571   0.703 0.812 0.701 ** 0.461 1.521
  ND4L 297 0.550   0.679 0.810 0.738 ** 0.472 1.564
  ND4 1377 0.612   0.654 0.936 0.722 ** 0.455 1.587
  ND5 1812 0.651   0.750 0.868 0.723 ** 0.471 1.535
  ND6 525 0.612   0.754 0.812 0.361   0.551 0.655
III CYTB 1134 0.655   0.711 0.921 0.758 ** 0.481 1.576
IV COX1 1542 0.644   0.750 0.859 0.715 ** 0.509 1.405
  COX2 684 0.641   0.713 0.899 0.664 ** 0.503 1.320
  COX3 780 0.656   0.725 0.905 0.704 ** 0.497 1.416
V ATP8 207 0.606   0.688 0.881 0.633 ** 0.452 1.400
  ATP6 681 0.629   0.698 0.901 0.701 ** 0.472 1.485
  1. Expected CAIs (eCAIs) at 95% (p = 0.05) and 99% (p = 0.01) confidence and 99% coverage were calculated using the Poisson method of the E-CAI server. For the sake of clarity, only the eCAI values at p = 0.05 are shown. CAIhm and CAImt mean CAI calculated using the mean nuclear and mitochondrial codon usage as a reference set, respectively. CAI values were calculated using the CAIcal tool http://genomes.urv.es/CAIcal.
  2. * and ** mean that the CAI is higher than the eCAI estimated at 95% (*) and 99% (**) confidence and 99% coverage. Normalised CAI values (defined as the quotient between the CAI and its expected value) bigger than one are in bold and must be interpreted as evidence of adaptation to the reference codon usage beyond mere compositional biases.