Element:Ty4

From The Gypsy Database

Description

Ty4 is representative of one of the four LTR retrotransposon sets (Ty1, Ty2, Ty3 and Ty4) described in the genome of yeast Saccharomyces cerevisiae (Boeke and Sandmeyer 1991; Janetzky and Lehle 1992). It shows the greatest similarity with Ty2 and Ty1 elements and with them represents one of the members of Ty (Pseudovirus) clade, one of the three original genera on which the in-progrees Pseudoviridae classification is constituted (Boeke et al 2005).

Ty4 genome is about of 6.2 Kb in size, including two 371-bp LTRs (Stucka et al. 1992; Janetzky and Lehle 1992). The LTRs flanked internal region contains two overlapping open reading frames (ORFs): the first ORF, TYA4, encodes a protein with the conserved motif (CCHC) found in the nucleic acid-binding gag-protein of retroviruses; the second ORF, TYB4, encodes a polyprotein showing domains with significant homology to the Ty1/Copia-like protease, integrase, reverse transcriptase, and RNase H (structurally arranged in this order) (Janetzky and Lehle 1992; Stucka et al. 1992). A potential primer binding site is located downstream to the 5’LTR, it differs from those of the other yeast Ty elements to be complementary to a tRNAAsn (Neuvéglise et al. 2002).

Structure

Ty4.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:1218005 (nts 153-6362)
Clade:Ty (Pseudovirus)
Cluster or genus:Pseudovirus
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Saccharomyces cerevisiae.gif
Saccharomyces cerevisiae
Image, Joaquin Panadero,
Copyright, GyDB, Biotech Vana
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