Element:Olco1

From The Gypsy Database

Description

Olco1, a Ty1/Copia-like LTR retrotransposon, is associated to the family of GalEa-like elements and has been described in the genome of the Japanese medaka fish (Oryzias latipes) (Terrat et al. 2008). Olco1 belongs to GalEA clade a Ty1/Copia lineage specifically found in marin animals (Terrat et al. 2008).

The genome of Olco1, of 4760 bp in size, includes LTRs of 187 bp long bounding an internal region that contains a Primer Binding Site (PBS) complementary to a tRNAMet, a single large Open Reading Frame (ORF) (which harbors a stop codon and a frameshift) and a Polypurine Tract (PPT) upstream its 3’LTR. The ORF displays the typical gag and pol polyprotein domains of Ty1/Copia LTR retrotransposons: gag, protease, integrase, reverse transcriptase and RNase H (Terrat et al. 2008).

Structure

Olco1.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:154726954
Clade:GalEA
Cluster or genus:Undetermined
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Oryzias latipes.jpg
Oryzias latipes
Courtesy of Prof. Shinichi Morishita, University of Tokyo
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