Element:Zeco2

From The Gypsy Database

Description

Zeco2 is a Ty1/Copia-like LTR retrotransposon described, together its closer related element Zeco1, in the genome of the zebrafish (Danio rerio) (Terrat et al. 2008). It belongs to GalEA clade a Ty1/Copia lineage specifically found in marin animals (Terrat et al. 2008).

The genome of Zeco2 is about of 4.8 Kb in size (4840 bp long) including a 204-bp 5’ LTR and a 197-bp 3’LTR that flank an internal coding region. Although this region is disrupted by a several stop codons and frameshifts, it displays the typical gag and pol domains associated to Ty1/Copia LTR retrotransposons. A Primer Binding Site (PBS) complementary to a tRNAMet and a Polypurine Tract (PPT) are located respectively downstream and upstream to the 5’LTR and 3’LTR (Terrat et al. 2008).

Structure

Zeco2.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:124597607
Clade:GalEA
Cluster or genus:Undetermined
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
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Danio rerio.jpg
Danio rerio
Image, courtesy of Wikipedia
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