Element:Copia

From The Gypsy Database

Description

Copia is a Ty1/Copia LTR retrotransposon abundantly represented in the genome of Drosophila spp (Peterson-Burch and Voytas 2002). The Copia element described in Drosophila simulans (Yoshioka et al. 1992) is taken as a representative. Copia belongs and gives the name to Copia clade, which is consistent with a genus within the current ICTV classification of the Ty1/Copia into three genera – Pseudovirus, Hemivirus and Sirevirus (Boeke et al. 2005).

Copia is 5165 kbp in size, including a 276-bp 5’-LTR and a 277-bp 3’LTR (Yoshioka et al. 1992)). The structure of this element contains a Primer Binding Site (PBS) for a tRNAMet, a single Open Reading Frame (ORF) of 1409 amino acids and a Polypurine Tract (PPT) preceding its 3’LTR. The ORF contains the typical gag-pol Ty1/Copia-like structure displaying the gag, protease, integrase, reverse transcriptase and ribonuclease H domains (Yoshioka et al. 1992).

Structure

Copia.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:391656
Clade:Copia
Cluster or genus:Hemivirus
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
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Drosophila melanogaster.gif
Drosophila spp.
Image, courtesy of Andreas Trepte, Max-Planck Institute for Molecular Genetics
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