Fig. 1.

Overview of L1 elements and methodology. a) Schematic of the (Khan et al. 2006) L1HS subfamily model, showing the locations of the ORFs and domains. Domains are labeled with black boxes, and according to their CDD names (note that these names are misnomers relative to current understanding of LINE-1s). In ORF1, “Transposase 22 dsRBD” is the CTD, “Transposase 22” is the RRM, and “Transposase 22 Trimer” the N-terminal section of the coiled-coil domain. The full length of the coiled-coil domain is indicated with diagonal hatching. b) Workflow used to annotate L1 loci in ancestral genomes and reconstruct L1 progenitors. The sequence logos represent segments of Dfam L1 profile HMMs.