Description
Kobel is a LTR retrotransposon characterized in the Hemichordata acorn worm Saccoglossus kowalevskii (Llorens et al. 2009). Its name is an acronym derived from Saccoglossus kowalevskii Bel/Pao element. Kobel belongs to the Sinbad clade (Copeland et al. 2005) within Branch 2 of the Bel/Pao LTR retrotransposon family (Llorens et al. 2009).
The genome of Kobel is 7471 bp in lenght, including LTRs of 865 nt. The internal region of this LTR retrotransposon displays a single ORF encoding for gag and pol genes. The gag polyprotein presents three CCHC (Cysteine zinc finger array) motifs characteristic of the nucleocapsid domain, while the pol contains the domains of the putative protease, reverse transcriptase, RNase H and integrase proteins (Llorens et al. 2009).
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
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PR=protease
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DU or DUT=dUTPase
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TM=transmembrane
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TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
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| CA=capsid
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RT=reverse transcriptase
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INT=Integrase
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CHR=chromodomain
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| NC=nucleocapsid
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RH=RNaseH
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SU=surface
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MOV=movement protein
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| PPT=polypurine tract
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PBS=primer binding site
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ATF=aphid transmission factor
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VAP=virion associated protein
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Related literature
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