From The Gypsy Database


CoDi4.4 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). It 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).

CoDi4.4 genome, of 6753 bp in size, includes a 153-bp 5’LTR and a 142-bp 3’LTR that flank 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:

MA=matrix PR=protease DU or DUT=dUTPase TM=transmembrane TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
CA=capsid RT=reverse transcriptase INT=Integrase CHR=chromodomain
NC=nucleocapsid RH=RNaseH SU=surface MOV=movement protein
PPT=polypurine tract PBS=primer binding site ATF=aphid transmission factor VAP=virion associated protein

Related literature

Genbank accession:169639613
Cluster or genus:Undetermined
Branch or class:Branch 1
System:LTR retroelements
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Phaeodactylum tricornutum2.jpg
Phaeodactylum tricornutum
Courtesy of Dr. Yves Van de Peer, VIB Department of Plant Systems Biology, UGent Ghent University
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