Element:RIRE2

From The Gypsy Database

Description

RIRE2 is a LTR retrotransposon described in the genome of Oryza sativa (Ohtsubo, Kumekawa and Ohtsubo 1999). This element belongs to a lineage of plant LTR retrotransposons (Tat), sibling of other lineage of putative plant endogenous retroviruses (Athila), providing evidence of a shared ancestral lineage originally described as class A by Wright and Voytas (1998). The genomic structure of RIRE2 is 11.2 Kb in size including LTRs of 441 nt. The internal region displays a Primer Binding Site (PBS) complementary to a tRNAArg, two Open Reading Frames (ORFs) for gag and pol genes, as well as three complementary ORFs named ORF5, ORF4, and ORF3 displayed between the integrase domain, and also, a Polypurine Tract (PPT) adjacent to the 3´LTR (Ohtsubo, Kumekawa and Ohtsubo 1999).

Structure

Rire2.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:AB030283
Clade:Tat
Cluster or genus:Athila/Tat
Branch or class:Branch 2
Family:Ty3/Gypsy
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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