Element:Opie-2

From The Gypsy Database

Description

Opie-2 is a Ty1/Copia LTR retrotransposon originally described in Zea mays (SanMiguel et al. 1996) and also found in rice (Oriza sativa, GenBank accession AC104473). Opie-2 belongs to SIRE a clade of Ty1/Copia plant LTR retrotransposons and potential retroviruses (Fauquet et al. 2005) evolutionarily related to another clade of plant Ty1/Copia LTR retrotransposons called Oryco (Llorens et al. 2009). SIRE clade 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 Opie-2 full-length genome is 11.7 Kb in size, comprising both long LTRs of 1375 (5’) and 1348 nts (3’). The size difference between both LTRs is due to some nucleotides deletions within 3’LTR sequence. The internal region of this element contains a Primer Binding Site (PBS) complementary to a tRNAiMet, a coding region and a final Polypurine Tract (PPT) (SanMiguel et al. 1996). Although the internal coding region is disrupted by several stop codons and frameshiftings (for simplicity´s sake, the figure below shows an idealized single ORF organization), the distinct gag and pol domains typical of Ty1/Copia elements are well preserved in this element. Similarly to other Sire elements, Opie-2 contains a putative env-like gene at its C-terminal translated region (SanMiguel et al. 1996). In comparison to other Ty1/Copia elements, a particular feature of Sire-like elements meriting attention is their extremely large gag c-terminus consistent with the NC domain, which may display two or three CCHC arrays (Llorens et al. 2009).

Structure

Opie-2.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:24080635
Clade:Sire
Cluster or genus:Sirevirus
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Oryza sativa.gif
Oryza sativa
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
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