Element:CoDi7.1

From The Gypsy Database

Description

CoDi7.1 is a Ty1/Copia LTR retrotransposon described in the genome of the marine pinnate diatom Phaeodactylum tricornutum (Maumus et al. 2009; Bowler et al. 2008). It belongs to CoDi-I clade (Maumus et al. 2009), within Branch 1 of the Ty1/Copia family, that represents an interesting group of elements carrying a putative chromodomain at the C-terminus of the pol-INT domain (Llorens et al. 2009), similar to those coded by almost all Ty3/Gypsy chromoviruses which probably use this feature for chromatin integration (Gao et al. 2008).


The genome of CoDi7.1, of about 6 kb in size (5954 bp long), includes 257-bp LTRs bounding a single long Open Reading Frame (ORF) of 1789 amino acids that 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

CoDi7-1.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:169639654
Clade:CoDi-I
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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