Element:CsRN1

From The Gypsy Database

Description

CsRN1 is a LTR retrotransposon characterized in the genome of Clonorchis sinensis (Bae et al. 2001). CsRN1 gives the name and belongs to CsRN1 clade (Bae et al. 2001). The genomic full-length consensus for CsRN1 is 5 Kb in size and flanked by LTRs which display an average size of 471 nt. The internal region of this element displays a Primer Binding Site (PBS) complementary to a tRNATrp, a sole Open Reading Frame (ORF) coding for a gag-pol precursor, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Bae et al. 2001).

Structure

Csrn1.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:AY013571
Clade:CsRN1
Cluster or genus:Undetermined
Branch or class:Branch 2
Family:Ty3/Gypsy
System:LTR retroelements
Host:
Explore the Tree Life Project
Clonorchis sinensis.gif
Clonorchis sinensis
Image, courtesy of John H. Wahlert et al., Baruch College
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