Element:Yokozuna

From The Gypsy Database

Description

Yokozuna is the first Ty1/Copia LTR retrotransposon characterized in the genome of the domestic silkworm, Bombyx mori (Ohbayashi et al. 1998). This element is part of a nested structure containing at least seven mobile elements, it is located in the Kabuki Ty3/Gypsy-like retroelement (Ohbayashi et al. 1998; Abe et al. 2000). Yokozuna is closely related (or tentatively belongs) to Copia clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). Yokozuna genome is 4738 bp in size, including a 208-bp 5’-LTR and a 183-bp 3’LTR. The different size is due to an insertion (or deletion) of 25 bp. These LTRs differ from other retrotransposable element LTRs in that they do not terminate in CA (Ohbayashi et al. 1998). The internal region of this element contains a Primer Binding Site (PBS), a single long Open Reading Frame (ORF) displaying the typical Ty1/Copia-like gag and pol domains (gag, protease, integrase, reverse transcriptase and ribonuclease H) and a Polypurine Tract (PPT) adjacent to the 3’ LTR (Ohbayashi et al. 1998).

Structure

Yokozuna.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

Mobile DNA II. (Craig et al. 2002)

Genbank accession:4239842
Clade:Copia
Cluster or genus:Hemivirus
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
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Bombyx mori.gif
Bombyx mori
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
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