Element:Vitico1-2

From The Gypsy Database

Description

Vitico1-2 is a LTR retrotransposon found in the genome of Vitis vinifera (Llorens et al. 2009). This element belongs to Retrofit clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). The genome of Vitico1-2 is 4752 bp in size, including LTRs of 299 (5’LTR) and 295 nts long (3’LTR). The complete sequence of this element corresponds to the Vitis vinifera genome region included between the nucleotides 1075 and 5826 (GenBank accession: 147783960). LTRs flank a coding region displaying both Ty1/Copia-like gag-pol polyproteins domains. Due to the presence of several stop codons and frameshiftings the sequence analyzed has been obtained by the assembly of adjacent polyprotein regions (GenBank accession: AM462010.2).

Structure

Vitico1-2.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:147783960
Clade:Retrofit
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Vitis vinifera.jpg
Vitis vinifera
Wikimedia, courtesy of "Bangin"
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