Element:Koco

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(koepferae Copia) is a Ty1/Copia LTR retrotransposon found in the genome of Drosophila koepferae (Francino and Cabre, Unpublished data, GenBank accession X96971).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 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 Mobile DNA II. (Craig et al. 2002)

Genbank accession: 1255921 Clade: Copia Cluster or genus: Hemivirus Branch or class: Branch 2 Family: Ty1/Copia System: LTR retroelements Host: Explore the Tree Life Project Drosophila spp. Image, courtesy of Andreas Trepte, Max-Planck Institute for Molecular Genetics Browse all elements