Element:CoDi5.4

From The Gypsy Database

Description

CoDi5.4 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).

CoDi5.4 genome, of 5376 bp in size, includes LTRs of 164 bp flanking an internal region that encodes a long 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 ribonuclease H (for more details, see Maumus et al. 2009).

Structure

CoDi5-4.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:169639628
Clade:CoDi-II
Cluster or genus:Undetermined
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Thalassiosira pseudonana.jpg
Thalassiosira pseudonana
Courtesy of Nils Kröger, Georgia Institute of Technology, Atlanta, USA
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