Element:CoDi5.5

Description

CoDi5.5 is a Ty1/Copia LTR retrotransposon described in the genome of the marine algae phytoplankton, Thalassiosira pseudonana (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).

The genome of CoDi5.5, of 5758 bp in size, includes LTRs of 246 nt bounding an internal region that encodes for two overlapping Open Reading Frames (ORFs). The first ORF contains the putative gag domains, while the second larger ORF displays the typical pol polyprotein structure of Ty1/Copia LTR retrotransposons (for more details, see Maumus et al. 2009).

Structure

CoDi5-5.png


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: 169639631
Clade: CoDi-II
Cluster or genus: Undetermined
Branch or class: Branch 1
Family: Ty1/Copia
System: LTR retroelements
Host:
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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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