Element:ToRTL1

Description ToRTL1 is a Ty1/Copia LTR retroelement found in tomato plants (Solanum lycopersicon, syn. Lycopersicon esculentum) (Peterson-Burch and Voytas, 2002; Havecker et al. 2005). ToRTL1 belongs to the SIRE clade of Ty1/Copia plant LTR retrotransposons and potential retroviruses (Peterson-Burch and Voytas, 2002; Havecker et al. 2005;Fauquet et al. 2005) evolutionarily related to another clade of plant Ty1/Copia LTR retrotransposons called Oryco (Llorens et al. 2009). SIRE clade gives the name to a genus within the current ICTV classification of the Ty1/Copia into three genera – Pseudovirus, Hemivirus and Sirevirus (Boeke et al. 2005). The full-lenght genome of ToRTL1 is 9688 bp in size, including LTRs of 808 (5’LTR) and 809 (3’LTR) bps long. The internal region contains a Primer Binding Site (PBS) complementary to a tRNAiMet, a coding region and a Polypurine Tract (PPT) upstream its 3’LTR. The coding region presents three Open reading frames (ORFs) that, although are disrupted by several stop codons and frameshiftings, show the distinct gag, pol and env-like genes characteristic of Sire elements (Peterson-Burch and Voytas, 2002; Havecker et al. 2005). In comparison to other Ty1/Copia elements, a taxonomically relevant feature specific of Sire-like elements is their extremely large gag c-terminus consistent with the NC domain, which may display two or three CCHC arrays (Llorens et al. 2009). 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 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 Mobile DNA II. (Craig et al. 2002)

Genbank accession: 2246449 Clade: Sire Cluster or genus: Sirevirus Branch or class: Branch 2 Family: Ty1/Copia System: LTR retroelements Host: Explore the Tree Life Project Lycopersicon esculentum Image, Laura Covelli, Copyright, GyDB, Biotech Vana Browse all elements