Element:Cer5

From The Gypsy Database

Description

Cer5 is a LTR retrotransposon described from sequencing data in the chromosomes I-II of C. elegans (Bowen and McDonald 1999). Cer5 belongs, along with other LTR retrotransposons, to Mag a large Ty3/Gypsy cluster widely distributed in both protostomes and deuterostomes (for more details, see Malik and Eickbush 1999; Volff et al. 2001; Tubio, Naveira and Costas 2004). Cer5 has at least two subtypes, Cer5-0 and Cer5-1, subtype Cer5-0 is taken as a representative. The genome of this clon is 5.1 Kb in size including LTRs of 211 nt. The internal region displays a Primer Binding Site (PBS) complementary to a tRNASer, a single Open Reading Frame (ORF) gag-pol, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Bowen and McDonald 1999; Ganko, Fielman and McDonald 2001).

Structure

Cer5.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:U88169 (nuc 9519-14600)
Clade:B-clade
Cluster or genus:Mag
Branch or class:Branch 2
Family:Ty3/Gypsy
System:LTR retroelements
Host:
Explore the Tree Life Project
Caenorhabditis elegans.gif
Caenorhabditis elegans
Image by courtesy of Ralf J. Sommer, Max Planck Institute for Developmental Biology
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