Element:Yokozuna

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 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: Explore the Tree Life Project Bombyx mori Image, Carlos Llorens, Copyright, GyDB, Biotech Vana Browse all elements