About: A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Long terminal repeat (LTR) retrotransposons make up substantial parts of most higher plant genomes where they accumulate due to their replicative mode of transposition. Although the transposition is facilitated by proteins encoded within the gag-pol region which is common to all autonomous elements, some LTR retrotransposons were found to potentially carry an additional protein coding capacity represented by extra open reading frames located upstream or downstream of gag-pol. In this study, we performed a comprehensive in silico survey and comparative analysis of these extra open reading frames (ORFs) in the group of Ty3/gypsy LTR retrotransposons as the first step towards our understanding of their origin and function. We found that extra ORFs occur in all three major lineages of plant Ty3/gypsy elements, being the most frequent in the Tat lineage where most (77 %) of identified elements contained extra ORFs. This lineage was also characterized by the highest diversity of extra ORF arrangement (position and orientation) within the elements. Long terminal repeat (LTR) retrotransposons make up substantial parts of most higher plant genomes where they accumulate due to their replicative mode of transposition. Although the transposition is facilitated by proteins encoded within the gag-pol region which is common to all autonomous elements, some LTR retrotransposons were found to potentially carry an additional protein coding capacity represented by extra open reading frames located upstream or downstream of gag-pol. In this study, we performed a comprehensive in silico survey and comparative analysis of these extra open reading frames (ORFs) in the group of Ty3/gypsy LTR retrotransposons as the first step towards our understanding of their origin and function. We found that extra ORFs occur in all three major lineages of plant Ty3/gypsy elements, being the most frequent in the Tat lineage where most (77 %) of identified elements contained extra ORFs. This lineage was also characterized by the highest diversity of extra ORF arrangement (position and orientation) within the elements. (en)
Title	A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons (en)
skos:prefLabel	A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons (en)
skos:notation	RIV/60077344:_____/11:00377346!RIV13-AV0-60077344
http://linked.open...avai/predkladatel	Biologické centrum AV ČR, v. v. i.
http://linked.open...avai/riv/aktivita	Z
http://linked.open...avai/riv/aktivity	Z(AV0Z50510513)
http://linked.open...iv/cisloPeriodika	11-12
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Steinbauerová, Veronika Neumann, Pavel Macas, Jiří Novák, Petr
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Biologické centrum AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	184258
http://linked.open...ai/riv/idVysledku	RIV/60077344:_____/11:00377346
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	Additional ORFs; LTR retrotransposons; Repetitive DNA; Plant genome (en)
http://linked.open.../riv/klicoveSlovo	Additional ORFs LTR retrotransposons Plant genome Repetitive DNA
http://linked.open...odStatuVydavatele	NL - Nizozemsko
http://linked.open...ontrolniKodProRIV	[FE5ADE68D4F8]
http://linked.open...i/riv/nazevZdroje	Genetica
http://linked.open...in/vavai/riv/obor	EB
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	139
http://linked.open...iv/tvurceVysledku	Macas, Jiří Novák, Petr Neumann, Pavel Steinbauerová, Veronika
http://linked.open...ain/vavai/riv/wos	000304136900017
http://linked.open...n/vavai/riv/zamer	Výzkum struktury genetické informace rostlin a jejich patogenů na molekulární úrovni, indukce a analýza cílených změn genomu a plastomu a studium fotosyntetických procesů a projevů dědičnosti v interakci s prostředím a patogeny
issn	0016-6707
number of pages	13 (xsd:int)
http://bibframe.org/vocab/doi	10.1007/s10709-012-9654-9
is http://linked.open...avai/riv/vysledek of	A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons

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