Element:Kobel

From The Gypsy Database

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

Kobel.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:154426342
Clade:Sinbad
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Bel/Pao
System:LTR retroelements
Host:
Explore the Tree Life Project
Saccoglossus.gif
Saccoglossus spp
Cortesy of Marine Biological Laboratory
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