Element:Tdh2

From The Gypsy Database

Description

Tdh2, a Ty1/Copia-like LTR retrotransposon characterized in the genome of the spoilage yeast Debaryomyces hansenii (Neuvéglise et al. 2002). This element belongs to Ty (Pseudovirus) clade one of the three original genera on which the in-progrees Pseudoviridae classification is constituted (Boeke et al 2005).

The genome of Tdh2 is 5928 bp in size, including two 379-bp LTRs that bound an internal coding region containing a Primer Binding Site (PBS), complementary to a tRNAArg, a long Open Reading Frame (ORF) interrupted by one stop codon, and a Polypurine Tract (PPT) upstream to the 3’LTR (Neuvéglise et al. 2002). The ORF shows the typical domains associated to Ty1/Copia gag and pol genes. The gag-associated RNA-binding motif (CCHC) has not been identified in this element (Neuvéglise et al. 2002).

Structure

Tdh2.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:20152518
Clade:Ty (Pseudovirus)
Cluster or genus:Pseudovirus
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
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Debaryomyces Hanserii.jpg
Debaryomyces Hanserii
Courtesy of Dr. Duong Van Hop Curator of the Vietnam Type Culture Collection Institute of Microbiology and Biotechnology Vietnam National University, Hanoi
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