https://gydb.org/index.php?action=history&feed=atom&title=Element%3AOpie-2Element:Opie-2 - Revision history2026-06-09T14:57:57ZRevision history for this page on the wikiMediaWiki 1.35.0https://gydb.org/index.php?title=Element:Opie-2&diff=616&oldid=previmported>Gydbwiki at 15:26, 13 January 20102010-01-13T15:26:22Z<p></p>
<p><b>New page</b></p><div>{{Element<br />
|genbank=[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=24080635 24080635]<br />
|type=Sire<br />
|genus=Sirevirus<br />
|subfamily=Branch 2<br />
|family= Ty1/Copia<br />
|group= LTR retroelements<br />
|description=''Opie-2'' is a ''Ty1/Copia'' LTR retrotransposon originally described in ''Zea mays'' ([[Literature: 66255|SanMiguel ''et al''. 1996]]) and also found in rice (''Oriza sativa'', GenBank accession [http://www.ncbi.nlm.nih.gov/nuccore/24080635?from=40919&to=49075&report=gbwithparts AC104473]). ''Opie-2'' belongs to SIRE a clade of ''Ty1/Copia'' plant LTR retrotransposons and potential retroviruses ([[Literature:100589|Fauquet ''et al.'' 2005]]) evolutionarily related to another clade of plant ''Ty1/Copia'' LTR retrotransposons called ''Oryco'' ([[Literature:100596|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 ([[Literature:100591|Boeke ''et al''. 2005]]). <br />
<br />
The ''Opie-2'' full-length genome is 11.7 Kb in size, comprising both long LTRs of 1375 (5’) and 1348 nts (3’). The size difference between both LTRs is due to some nucleotides deletions within 3’LTR sequence. The internal region of this element contains a Primer Binding Site (PBS) complementary to a tRNA<sup>iMet</sup>, a coding region and a final Polypurine Tract (PPT) ([[Literature: 66255|SanMiguel ''et al''. 1996]]). Although the internal coding region is disrupted by several stop codons and frameshiftings (for simplicity´s sake, the figure below shows an idealized single ORF organization), the distinct ''gag'' and ''pol'' domains typical of ''Ty1/Copia'' elements are well preserved in this element. Similarly to other ''Sire'' elements, ''Opie-2'' contains a putative ''env''-like gene at its C-terminal translated region ([[Literature: 66255|SanMiguel ''et al''. 1996]]). In comparison to other ''Ty1/Copia'' elements, a particular feature of ''Sire''-like elements meriting attention is their extremely large gag c-terminus consistent with the NC domain, which may display two or three CCHC arrays ([[Literature:100596|Llorens ''et al''. 2009]]). <br />
|structure=opie-2.png<br />
|host=Oryza sativa<br />
|hostpic=Oryza_sativa.gif<br />
|literature=*[[Literature:15303|Mobile DNA II. (Craig et al. 2002)]]<br />
|picowner=[http://www.biotechvana.com Image, Carlos Llorens, <br>Copyright, GyDB, Biotech Vana]<br />
}}<br />
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