Element:Poco

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 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: 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 Wikipedia, courtesy of Walter Siegmund Browse all elements