Element:Oryco1-1

From The Gypsy Database

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

Oryco1-1.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:41223814 (nuc 12146-17072)
Clade:Oryco
Cluster or genus:Undetermined
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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