Element:Gmr1

From The Gypsy Database

Description

Gmr1 is a unsual Ty3/Gypsy LTR retrotransposon described (between two immunoglobulin light-chain L1 regions) in the genome of the Atlantic cod Gadus morhua, together with other elements from diverse vertebrates, including the zebrafish Danio rerio and Xenopus (Butler et al. 2001; Goodwin and Poulter 2002). These constitute an own clade (to which Gmr1 gives the name) possibly related via sequence similarity with Osvaldo clade (Butler et al. 2001; Goodwin and Poulter 2002; Llorens et al. 2009). Interestingly, Gmr1 elements differ from other Ty3/Gypsy LTR retroelements in the fact that the integrase domain lies upstream of the reverse transcriptase domain, an arrangement which is characteristic of Ty1/Copia LTR retroelements (Butler et al. 2001; Goodwin and Poulter 2002).

The genomic structure of Gmr1 is 8 Kb in size including LTRs of approximately 1 Kb in size. The internal region of this element displays a Primer Binding Site (PBS) complementary to a tRNAala, an Open Reading Frame (ORF) for gag and protease displaying a frameshifting and overlapping with the integrase ORF which shows a frameshifting and another ORF for reverse transtriptase and RNAseH. The element shows the typical Polypurine Tract (PPT) adjacent to the 3´LTRs (Butler et al. 2001;Goodwin and Poulter 2002).

Structure

Gmr1.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:4378494
Clade:Gmr1
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty3/Gypsy
System:LTR retroelements
Host:
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Gadus morhua.jpg
Gadus morhua
Wikipedia, courtesy of Hans-Petter Fjeld (CC-BY-SA)
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