Figure 2

ORF1 types identified in the Jockey, CR1 and L2 lineages. Subtypes (A, B, C) are used to show the diversity of ORF1 structures within types identified in this paper. Subtype titles within a circle denote those previously described by Khazina and Weichenrieder [11] and Kapitonov et al. [16]. Lineages and subgroups were identified by ORF1 structure and phylogenetic structuring based on the apurinic endonuclease (APE) and reverse transcriptase (RT) domains (see Figures 3, 4). Clades within lineages were identified by the RTclass1 tool [9]. The phylum and species are taken from the Repbase sequence title [17]. The ORF1 structure schematic shows coding domains 5’ to the endonuclease identified in this publication and are drawn to scale. Domains not always present are shown with a dashed outline. Red: CCHC, gag-like Cys₂HisCys zinc-knuckle; green: CTD, C terminal domain; yellow: coiled-coil domain; purple: esterase; pink: PHD, plant homeodomain; blue: RRM, RNA recognition motif; lilac: zf/lz, zinc finger/leucine zipper. The hatched CC, RRM + CTD domains indicate transposase 22, the RCSB Protein Data Bank entry 2yko and Pfam entry PF02994. A key to all the domains is shown in Figure 6.