Element:Oryco1-2

From The Gypsy Database

Description

Oryco1-2 (Oryza Copia element type 1-2) is an Oryco-like Ty1/Copia-like LTR retrotransposon described in the genome of rice (Oryza sativa ssp japonica) (Llorens et al. 2009). The genome of Oryco1-2 is 4938 bp in size, including LTRs of 163 nts that flank a coding region displaying an ORF coding for a single gag-pol product displaying the the typical Ty1/Copia-like ORF organization.

Structure

Oryco1-2.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:32488601 (nuc 10045-14982)
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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