Element:CoDi6.4

From The Gypsy Database

Description

CoDi6.4 is a Ty1/Copia-like LTR retrotransposon described in the genome of the marine pinnate diatom Phaeodactylum tricornutum (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.

The genome of CoDi6.4 is 5237 bp in size, including LTRs of 413 nts. The internal region of this element encodes for a single Open Reading Frame (ORF) of 1441 amino acids containing the typical gag-pol domains organization of Ty1/Copia LTR retrotransposons: gag (displaying two zing-finger motifs), protease, integrase, reverse transcriptase and RNase H. For more details, see (Maumus et al. 2009).

Structure

CoDi6-4.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:169639644
Clade:CoDi-D
Cluster or genus:Undetermined
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Phaeodactylum tricornutum2.jpg
Phaeodactylum tricornutum
Courtesy of Dr. Yves Van de Peer, VIB Department of Plant Systems Biology, UGent Ghent University
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