Element:RTvr2

From The Gypsy Database

Description

RTvr1 and RTvr2 are two Ty1/Copia-like retrotransposons characterized in the genome of the mung bean (Vigna radiata) (Xiao et al. 2007). They have been the first complete elements to be reported in this legume. RTvr2, is taken as a reference sequence as RTvr1 and RTvr2 elements display each other 92% of similarity (Xiao et al. 2007).Phylogenetic analyses reveal how this element belongs to Tork clade within the Branch 2 of Ty1/Copia family (Llorens et al. 2009).

RTvr2 genome is 7837 bp in size, including a 677-bp 5’LTR and a 676-bp 3’LTR that flank an internal coding region. The translated region reveals the presence of several stop codons therefore the putative Ty1/Copia-like gag and pol polyproteins derive from frameshiftings at certain positions (Xiao et al. 2007). A Primer Binding Site (PBS) and a Polypurine tract (PPT) are respectively downstream and upstream the 5’LTR and 3’LTR.

Structure

RTvr2.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:59380637
Clade:Tork
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
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Vigna radiata.jpg
Vigna radiata
Wikimedia, courtesy of "Sarefo"
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