Element:Cer1

From The Gypsy Database

Description

Cer1 is a Ty3/Gypsy LTR retroelement originally characterized as an integrate of the chromosome III of Caenorhabditis elegans (Britten 1995; Bowen and McDonald 1999). To date, no other homologues of Cer1 have been described. However, phylogenetic analyses based on both gag and pol polyproteins suggest that Cer1 might be a distantly related of Cer2-3 clade (see gag-pro-pol tree in section "phylogenies"). The genomic structure of Cer1 is 8.9 Kb in size including LTRs of 492 nt. The internal region of this element displays a Primer Binding Site (PBS) complementary to a tRNA Lys-Pro, a single Open Reading Frame (ORF) coding for a gag-pol polyprotein, and a Polypurine Tract (PPT) adjacent to the 3′LTR (Britten 1995). Cer1 also presents C-terminal and in frame with the integrase domain, an env-like domain already under study (Britten 1995).

Structure

Cer1.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:U15406
Clade:Cer1
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty3/Gypsy
System:LTR retroelements
Host:
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Caenorhabditis elegans.gif
Caenorhabditis elegans
Image, courtesy of Ralf J. Sommer, Max Planck Institute for Developmental Biology
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