Figure 4
From: Plant centromeric retrotransposons: a structural and cytogenetic perspective
Structural analysis of CRM elements. (A) Polyprotein coding (white boxes), noncoding (gray boxes), putative targeting domain (PTD) (hatched boxes) and long terminal repeats (LTRs) (arrowed). Pbs, primer binding site; ppt, polypurine tract; aaa, A-rich stretch. The group A member coding region extends into the 3' LTR, which encodes the CR motif. Group B elements lack any PTD. Group C possesses a type II chromodomain-coding domain which terminates close to the 5' end of the 3' LTR. The graph is not drawn in proportion to segment lengths in base pairs. (B) Most elements share TGATG and T/CATCA inverted repeats at, respectively, the 5' and 3' end of the LTR. The primer binding site complementary to the 3' end of tRNAMet differs in sequence between various families. Group A elements contain highly conserved polypurine tract sequences. (C) A protein similarity plot shows that the CRM polyproteins are highly conserved, varying mainly within their C-terminal PTD regions. Individual polyprotein domains: GAG, capsid domain, similar to pfam37032; ZF, nucleocapsid GAG protein zinc finger; PRO, protease; RT, reverse transcriptase RNase H; IN, integrase; PTD, putative targeting domain.