CoDi4.3 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-I clade (Maumus et al. 2009) within Branch 1 of the Ty1/Copia family (Llorens et al. 2009). Interestingly, CoDi-I represents the first described set of Ty1/Copia elements carrying a putative chromodomain at the C-terminus of the pol-INT domain (Llorens et al. 2009) similarly to Ty3/Gypsy chromoviruses (Marin and Lloréns 2000), which use this feature for chromatin integration (Gao et al. 2008).
The genome of CoDi4.3 is 6720 bp in size including LTRs of 162 bp that flank an internal coding region. The genome encodes for a long Open Reading Frame (ORF), interrupted by one stop codon, displaying 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