Element:Hopscotch

From The Gypsy Database

Description

Hopscotch is a Ty1/Copia LTR retrotransposon originally described in Zea mays (White et al. 1994) and also found in rice (Oryza sativa) (GenBank accession AC084320). Hopscotch belongs to the Retrofit clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). The genome of Hopscotch is 4.8 Kb in size (4800 bp long) and presents an internal coding region disrupted by several stop codons but displaying the typical gag and pol domains associated to Ty1/Copia LTR retrotransposons (no information about LTRs is yet available).

Structure

Hopscotch.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:20198550
Clade:Retrofit
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Oryza sativa.gif
Oryza sativa
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
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