BMC Genomics 2005, 6:136 http://www.biomedcentral.com/1471-2164/6/136 Table 2: Base composition at each codon position in mtDNA-encoded membrane and soluble protein-coding transcripts. Analysis was performed on transcripts from humans and the species from Table 1 that encode soluble proteins in mtDNA. Membrane Proteins Soluble Proteins Saccharomyces cerevisiae Codon pos. 1 Codon pos. 2 Codon pos. 3 All Arabidopsis thaliana Codon pos. 1 Codon pos. 2 Codon pos. 3 All Porphyra purpurea Codon pos. 1 Codon pos. 2 Codon pos. 3 All Dictyostelium discoideum Codon pos. 1 Codon pos. 2 Codon pos. 3 All Chondrus crispus Codon pos. 1 Codon pos. 2 Codon pos. 3 All Marchantia polymorpha Codon pos. 1 Codon pos. 2 Codon pos. 3 All Metridium senile Codon pos. 1 Codon pos. 2 Codon pos. 3 All Chlamydomonas reinhardtii Codon pos. 1 Codon pos. 2 Codon pos. 3 All Homo sapiens Codon pos. 1 Codon pos. 2 Codon pos. 3 All %A 28.1 21.3 42.9 30.7 26 21.5 26.5 24.7 30.8 21.5 34.9 29.1 35.9 25.7 57.8 39.8 30.5 21.4 35.9 29.3 27 20.8 28.5 25.4 21.7 25.9 26.4 24.6 24.7 16.4 15.5 18.9 29.5 22.8 34.3 28.9 %G 26.4 12.6 5.14 14.7 27.6 17.7 17.8 21 23.4 14.6 11.4 16.5 28.3 15.3 7.24 16.9 20.3 13.5 7.92 13.9 28.5 16.5 14.6 19.8 18.5 17.7 25.1 20.4 30.5 19.3 19.8 23.2 19.6 11.4 8.38 13.1 %C 10.3 22 7.49 13.3 20.5 23.7 17.5 20.5 14.7 20.9 15.4 17 7.92 15.9 4.83 9.55 13.8 19.8 7.75 13.8 16 21.1 13.9 17 19.8 16.4 14.7 17 17.5 21.5 26.3 21.8 26.9 29.9 39 31.9 %T 35.2 44.1 44.5 41.3 26 37.2 38.2 33.8 31.1 43 38.3 37.5 27.9 43.1 30.2 33.7 35.4 45.3 48.4 43.1 28.6 41.6 43 37.7 40 40 33.8 37.9 27.2 42.8 38.4 36.1 24 36 18.4 26.1 %Pu 54.5 33.9 48 45.5 53.6 39.2 44.3 45.7 54.2 36.1 46.3 45.5 64.2 41 65 56.7 50.8 34.9 43.8 43.2 55.5 37.3 43.1 45.3 40.2 43.6 51.5 45.1 55.2 35.8 35.3 42.1 49.1 34.2 42.7 42 %AT 63.3 65.3 87.4 72 51.9 58.6 64.8 58.4 61.9 64.4 73.2 66.5 63.8 68.8 87.9 73.5 65.9 66.7 84.3 72.3 55.5 62.4 71.5 63.2 61.7 65.9 60.2 62.6 51.9 59.2 53.9 55 53.5 58.8 52.7 55 %A 42.5 36.4 42.5 40.5 33 29 29.8 30.6 41.8 37.6 39.9 39.8 45.4 39.4 61.2 48.7 41.8 35.7 46 41.2 35.2 32.7 36 34.6 30.4 31.7 39.3 33.8 25.2 34.1 21.7 27 %G 20 13.3 4.57 12.6 26 22 22.2 23.4 21.2 14.9 12.2 16.1 23.6 17.7 10.1 17.2 16.1 13.9 6.81 12.3 23 19.6 15.3 19.3 28.1 20.1 13.4 20.5 24.4 14.4 23.6 20.8 %C 8.5 15 3.9 9.2 22 22 22 22 14 18 14 15 11 13 4.1 9.1 14 17 7.2 13 19 19 13 17 17 17 11 15 32 19 24 25 %T 29.1 35.3 49 37.8 19.1 27.4 26.3 24.3 23.1 29.4 34 28.8 20.4 30.1 24.6 25 28.5 33.6 40 34 22.9 28.5 35.3 28.9 24.6 30.8 36.6 30.7 18.7 32.8 31.2 27.6 %Pu 62.4 49.6 47.1 53.1 59.1 51 51.9 54 63 52.5 52.1 55.9 69 57.2 71.3 65.8 57.9 49.6 52.8 53.4 58.2 52.3 51.3 53.9 58.5 51.8 52.7 54.3 49.6 48.5 45.3 47.8 %AT 71.6 71.6 91.5 78.3 52.1 56.5 56.1 54.9 64.9 67.1 73.9 68.6 65.8 69.6 85.8 73.7 70.3 69.3 86 75.2 58.1 61.1 71.3 63.5 54.9 62.5 75.9 64.4 43.9 66.9 52.8 54.6 ever, the ND6 transcript is pyrimidine-rich in other mam- mals even though it is encoded on the (+) light strand (see Table 1). The percent occurrence of each individual nucle- otide species in each codon position in mitochondrial genomes from many eukaryotic species is given in Table 2. It is shown that C more than T in codon positions 1 and 3 drives the pyrimidine-rich signal in human membrane protein transcripts, while T more than C at codon position 2 also contributes. The constancy of this pattern through- out the genes as well as the overall abundance of A over G and C over T can be observed in 2-dimensional walks of the individual codon positions and entire transcripts (see additional file 1: Figure S2). The pyrimidine-rich signal is driven by C over T only in birds, reptiles, and some mam- malian species. In all other species examined, T drives the signal from all 3 codon positions. Page 9 of 12 (page number not for citation purposes)