Bousios et al. BMC Genomics 2010, 11:89 http://www.biomedcentral.com/1471-2164/11/89 Page 5 of 14 Figure 2 The organization of the linker domain/3’LTR junction of Ty1/copia retrotransposons. (A) Genome structure of Ty1/copia retrotransposons, of which Sireviruses may contain an envelope-like gene. (B, C) Organization of the Sirevirus and classic elements linker domain/3’LTR junction. The IR arms (yellow) surround the loop sequence, of which the terminal PPT octamer (red) occupies the outmost 5’ side. Classic elements with nucleotides in bold indicate the region, where the left arm is located at the 3’ end of the pol gene region, due to the very short linker domain. the upstream PPTs is highly variable, as only four octa- mers (out of 63) employ an AT dinucleotide, of which none is linked with the TG motif that would create a puta- tive functional attachment site. In contrast, classic retro- transposons have a highly variable attachment site, with some elements lacking intervening bases between the terminal PPT and the 3’LTR (Figure 2c and Figure 3). A precisely positioned inverted repeat surrounds the PPT/3’LTR junction of Sireviruses and some classic retrotransposons As previously mentioned, TEIRESIAS included bases immediately upstream of the terminal PPT within the most conserved motif of the Sirevirus genome. Subsequent analysis revealed that this upstream region constitutes the 3’ section of a sequence (left IR arm), which is found inverted within the 3’LTR (right IR arm). The IR is present in all but three elements (Osr8, Endo- vir1-1 and ATCopia43) and shares high nucleotide iden- tity even between Sireviruses that colonize evolutionary distant monocot and eudicot plant species (Figure 2b). The main characteristic of the motif is the precise posi- tion of the left arm, which always borders the PPT octa- mer. The intervening ‘loop’ sequence is short in length and consists in a 5’ to 3’ direction of the terminal PPT, the 5’-AT/TG-3’ attachment site and the beginning of the 3’LTR, which is diverse with large parts often deleted. The right arm starts on average 28 bp inside