Poco (Populus Copia element) is a Ty1/Copia LTR retrotransposon found in the genome of the deciduous broadleaf tree "black cottonwood" (Populus trichocarpa) (Llorens et al. 2009). This element belongs to Oryco clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). The genome of Poco is about of 4.2 Kb in size (4281 bp long), including a 237-bp 5’LTR and a 306-bp 3’LTR. Their different size is due to a deletion (or insertion) of 69 bp. The LTRs flank two overlapping Open Reading Frames (ORFs) that display the typical gag and pol domains organization of Ty1/Copia LTR retrotransposons (gag, protease, integrase, reverse transcriptase and ribonuclease H).
Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:
||DU or DUT=dUTPase
||TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
||PBS=primer binding site
||ATF=aphid transmission factor
||VAP=virion associated protein