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).



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: 2246449
Clade: Sire
Cluster or genus: Sirevirus
Branch or class: Branch 2
Family: Ty1/Copia
System: LTR retroelements
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Solanum lycop.jpg
Lycopersicon esculentum
Image, Laura Covelli,
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Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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