Comparison of the structures of a typical autonomous animal Helitron, a potential intermediate from Phytophthora infestans , Helitron2 from Chlamydomonas reinhardtii , and an autonomous Helentron family from Nematostella vectensis . (A) The structure of a representative autonomous animal Helitron. (B) The structure of the putative Helentron intermediate identified from the Phyotophthora infestans genome. (C) The structure of a Helitron 2 family (redrawn from ). (D) The structure of an autonomous Helentron. The colored boxes represent the different encoded putative proteins or domains. The open black box denotes the ORF encoding the Rep/Helicase protein (the lighter green is the Rep, the medium green is the helicase, and the endonuclease is the darker olive shade). The orange block denotes the ORF encoding the RPA protein. The purple box represents the SET domain, blue box represents the OTU-like cysteine proteases, pink and yellow boxes represent the hypothetical proteins. Proteins and/or domains are included only if they were found in multiple families or across species. The proteins that are occasionally carried by Helentrons are indicated with a black asterisk (*). The green arrows denote the subterminal inverted repeats (subTIRs). The green sideways triangle in the 5' end represents the 3' side of the inverted repeat (IR) (the 5' side is nested inside the 5' subTIR). The red stem loop denotes the palindrome at the 3' end. The flanking nucleotides are shown in red.