Element:PyRE1G1

From The Gypsy Database

Description

PyRE1G1 is a LTR retroelement described in the red macro alga Porphyra yezoensis (Peddigari et al. 2008). It gives the name and constitutes a single clade within Branch 2 of the Ty1/Copia LTR retrotransposons family (Llorens et al. 2009). The full-length PyRE1G1 genome is 4807 bp in size, including two almost identical (except for a single nucleotide) 204-bp LTRs. The internal region of this element contains a single long Open Reading Frame (ORF) upstream and downstream flanked respectively by a Primer Binding Site (PBS) and a Polypurine Tract (PPT). The ORF encodes for the typical gag and pol domains of Ty1/Copia LTR retrotransposons genes: gag (in which is present the zinc finger motif of Cys-His type characteristic of the nucleocapside domain), protease, integrase, reverse transcriptase and RNase H (Peddigari et al. 2008).

Structure

PyRE1G1.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:208968931
Clade:PyRE1G1
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
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Porphyra yezoensis.jpg
Porphyra yezoensis
Courtesy of Wikipedia
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