Element:Tork4

From The Gypsy Database

Description

Tork4 is a Ty1/Copia LTR retrotransposon identified in tomato (Solanum lycopersicon syn. Lycopersicon esculentum) (Kalendar et al. 2007, unpublished). It belongs and gives the name to the Tork clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009).

The genome of Tork4 is 4867 bp in size, including two identical 398-bp LTRs that flank a single Open Reading Frame (ORF) of 1307 amino acids containing the typical gag-pol structure of Ty1/Copia LTR retrotransposons (gag, protease, integrase, reverse transcriptase and ribonuclease H).

Structure

Tork4.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:157060692
Clade:Tork
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Solanum lycop.jpg
Solanum lycopersicum
Image, Laura Covelli,
Copyright, GyDB, Biotech Vana
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