Description
Oryco1-1 (Oryco Copia element type 1-1) is a Ty1/Copia-like LTR retrotransposon found in the genome of the rice (Oryza sativa ssp. japonica) (Llorens et al. 2009). It belongs and gives the name to Oryco clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). The genome of Oryco1-1 is 4927 bp in size, including a 364-bp 5’LTR and a 366-bp 3’LTR. The LTRs flank an internal region containing two overlapping Open Reading Frames (ORFs) that display the typical gag and pol domains organization of Ty1/Copia LTR retrotransposons (gag, protease, integrase, reverse transcriptase and ribonuclease H).
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
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PR=protease
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DU or DUT=dUTPase
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TM=transmembrane
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TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
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| CA=capsid
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RT=reverse transcriptase
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INT=Integrase
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CHR=chromodomain
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| NC=nucleocapsid
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RH=RNaseH
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SU=surface
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MOV=movement protein
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| PPT=polypurine tract
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PBS=primer binding site
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ATF=aphid transmission factor
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VAP=virion associated protein
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Related literature
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