The tRNA nomenclature and the gene order of vertebrate mtDNA.

<p>Ac, pair of the acceptor stem; dh, pair of the DHU stem; an, pair of the anticodon stem; tp, pair of the TΨC stem. The numbering of pairs follows a 5’ → 3’ orientation. The 5’ nucleotide of a pair is marked with a, while the 3’ base is marked with b. The numbering scheme of Sprinzl et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158129#pone.0158129.ref020" target="_blank">20</a>] is provided only for the stems. Base pairings are indicated as follows: –, canonical Watson-Crick base pairing; •, base pairing involving G and T; |, base pairing implying a mismatch. A The gene order of vertebrate mtDNA is depicted at the bottom, linearised starting from <i>cox1</i>. Genes encoded on the α-strand (right to left orientation) are underlined in green, while those encoded on the β-strand are underlined in red (left to right orientation). Gene nomenclature: <i>atp6</i> and <i>atp8</i>: ATP synthase subunits 6 and 8; <i>cob</i>: apocytochrome b; <i>cox1</i>-<i>3</i>: cytochrome c oxidase subunits 1–3; <i>nad1-6</i> and <i>nad4L</i>: NADH dehydrogenase subunits 1–6 and 4L; <i>rrnS</i> and <i>rrnL</i>: small and large subunit ribosomal RNA (rRNA) genes; and X: transfer RNA (tRNA) genes, where X is the one-letter abbreviation of the corresponding amino acid. In particular, L1 identifies the CTN codon family; L2 the TTR codon family, S1 the AGY codon family, and S2 the TCN codon family. CR, Control Region.