Element:CoDi6.2

Description CoDi6.2 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). 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. CoDi6.2 genome is about 5.2 Kb in size. It includes LTRs of 242 nts flanking an internal region that encodes a long Open Reading Frame (ORF) of 1506 amino acids. The ORF contains the gag and pol typical domains 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). Structure 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 Mobile DNA II. (Craig et al. 2002)

Genbank accession: 169639640 Clade: CoDi-D Cluster or genus: Undetermined Branch or class: Branch 1 Family: Ty1/Copia System: LTR retroelements Host: Explore the Tree Life Project Thalassiosira pseudonana Courtesy of Nils Kröger, Georgia Institute of Technology, Atlanta (USA)) Browse all elements