Element:SIRE1-4

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 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 Mobile DNA II. (Craig et al. 2002)

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 Image, Carlos Llorens, Copyright, GyDB, Biotech Vana Browse all elements