From The Gypsy Database


CoDi6.1 is a Ty1/Copia-like LTR retrotransposon described in the genome of the marine algae phytoplankton, Thalassiosira pseudonana (Maumus et al. 2009; Bowler et al. 2008). We use the term CoDi-C (Llorens et al. 2009) to phylogenetically differentiate the two clades constituted by the distinct CoDi-6-like elements described by Maumus et al. (2009) in Phaeodactylum tricornutum and Thalassiosira pseudonana

CoDi6.1 genome, of 6957 bp in size, includes LTRs of 431 nt flanking an internal region that encodes a single Open Reading Frame (ORF) interrupted by one stop codon. The ORF contains the gag and pol typical structure of the Ty1/Copia LTR retrotransposons: gag, protease, integrase, reverse transcriptase and RNase 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:169639637
Cluster or genus:Undetermined
Branch or class:Branch 1
System:LTR retroelements
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Thalassiosira pseudonana.jpg
Thalassiosira pseudonana
Courtesy of Nils Kröger, Georgia Institute of Technology, Atlanta (USA))
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