CoDi6.3 is a Ty1/Copia-like LTR retrotransposon described together with several other Ty1/Copia elements termed CoDi-like in the genome of the marine algae phytoplankton Thalassiosira pseudonana (Maumus et al. 2009; Bowler et al. 2008). Subsequent We use the term CoDi-D (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.

CoDi6.3 genome is about 5.1 Kb in size (5182 bp long), includes small LTRs of 161 nts that bound an internal region that encodes a long Open Reading Frame (ORF) of 1488 amino acids. This ORF contains both gag and pol typical structure of the Ty1/Copia LTR retrotransposons: gag (displaying two zing-finger motifs), 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: 169639642
Clade: CoDi-D
Cluster or genus: Undetermined
Branch or class: Branch 1
Family: Ty1/Copia
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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Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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