Element:Koco

From The Gypsy Database

Description

Koco (koepferae Copia) is a Ty1/Copia LTR retrotransposon found in the genome of Drosophila koepferae (Francino and Cabre, Unpublished data, GenBank accession X96971). This element belongs to Copia clade, which gives the name to a genus within the current ICTV classification of the Ty1/Copia into three genera – Pseudovirus, Hemivirus and Sirevirus (Boeke et al. 2005).

The genome of Koco is 4982 bp in size, including LTRs of 248 (5’LTR) and 247 nts long (3’LTR). This element contains a Primer Binding Site (PBS) for a tRNAMet, two overlapping Open Reading Frames (ORFs) containing the typical gag and pol domains of Ty1/Copia LTR retrotransposons: gag, protease, integrase, reverse transcriptase and ribonuclease H; and a Polypurine Tract (PPT) upstream its 3’ LTR (see also, Llorens et al. 2009).

Structure

Koco.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:1255921
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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