Element:SIRE1-4

From The Gypsy Database

Description

SIRE1 is a Ty1/Copia LTR retroelement described in the genome of Glycine max (Laten 1999). SIRE1 belongs to SIRE a clade of Ty1/Copia plant LTR retrotransposons and potential retroviruses (Fauquet et al. 2005) evolutionarily related to another clade of plant Ty1/Copia LTR retrotransposons called Oryco (Llorens et al. 2009). SIRE clade gives the name to a genus within the current ICTV classification of the Ty1/Copia into three genera – Pseudovirus, Hemivirus and Sirevirus (Boeke et al. 2005).

The genome structure of SIRE1-4 (taken as a SIRE1 representative) is 9.8 Kb in size (9805 bp in length) including two long LTRs of 1148 bp (Laten et al. 2003). The internal region of this element contains a Primer Binding Site (PBS), complementary to a tRNAiMet, two Open Reading Frames (ORFs) and a Polypurine Tract (PPT). The largest first ORF contains a gag-pol gene encoding for the tyìcal gag and pol protein domains (gag, protease, integrase, reverse transcriptase and RNase H). This ORF is followed by a second ORF separated by a single stop codon that encodes for a putative env protein (Laten et al. 2003). In comparison to other Ty1/Copia elements, a taxonomically relevant feature specific of Sire-like elements is their extremely large gag c-terminus consistent with the NC domain, which may display two or three CCHC arrays (Llorens et al. 2009).

Structure

Sire1-4.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:29423269
Clade:Sire
Cluster or genus:Sirevirus
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Glycine max.gif
Glycine max
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
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