Element:CoDi4.1

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Description

CoDi4.1 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 (Llorens et al. 2009). Interestingly, CoDi-I represents the first described set of Ty1/Copia elements carrying a putative chromodomain at the C-terminus of the pol-INT domain (Llorens et al. 2009) similarly to Ty3/Gypsy chromoviruses (Marin and Lloréns 2000), which use this feature for chromatin integration (Gao et al. 2008).

The genome of CoDi4.1 is 7254 bp in size including LTRs of 300 bp that flank an internal region. The genome encodes for a long Open Reading Frame (ORF) interrupted by one stop codon that displays 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

CoDi4-1.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: 169639607
Clade: CoDi-I
Cluster or genus: Undetermined
Branch or class: Branch 1
Family: Ty1/Copia
System: LTR retroelements
Host:
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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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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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