Element:Poco

From The Gypsy Database

Description

Poco (Populus Copia element) is a Ty1/Copia LTR retrotransposon found in the genome of the deciduous broadleaf tree "black cottonwood" (Populus trichocarpa) (Llorens et al. 2009). This element belongs to Oryco clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). The genome of Poco is about of 4.2 Kb in size (4281 bp long), including a 237-bp 5’LTR and a 306-bp 3’LTR. Their different size is due to a deletion (or insertion) of 69 bp. The LTRs flank two overlapping Open Reading Frames (ORFs) that display the typical gag and pol domains organization of Ty1/Copia LTR retrotransposons (gag, protease, integrase, reverse transcriptase and ribonuclease H).

Structure

Poco.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:157365037 (nuc 45758-50038)
Clade:Oryco
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Populus trichocarpa.jpg
Populus trichocarpa
Wikipedia, courtesy of Walter Siegmund
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