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CoDi5.2 is a Ty1/Copia LTR retrotransposon described in the genome of the marine pinnate diatom Phaeodactylum tricornutum (Maumus et al. 2009; Bowler et al. 2008). This element belongs to CoDi-II clade (Maumus et al. 2009) within Branch 1 of the Ty1/Copia family (Llorens et al. 2009).
CoDi5.2 genome, of 5670 bp in size, includes LTRs of 308 bp flanking an internal region that encodes for two overlapping Open Reading Frames (ORFs) showing the gag and pol typical structure of the Ty1/Copia LTR retrotransposons: gag, protease, integrase, reverse transcriptase and ribonuclease H (for more details, see Maumus et al. 2009).
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