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RetrOryza specifications

Information


Unique identifier OMICS_15007
Name RetrOryza
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No
Wikipedia https://en.wikipedia.org/wiki/RetrOryza

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Publication for RetrOryza

RetrOryza citations

 (6)
call_split

miR2118 triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

2016
PMCID: 4788661
PMID: 26969003
DOI: 10.1186/s12284-016-0082-9
call_split See protocol

[…] ocess using successive hierarchical BLAST (Additional file ) versus (in order) miRBase v17.0 (Kozomara and Griffiths-Jones ), Rfam v7, a home-made repeat database (successive curated concatenation of RetrOryza, RepBase, TREP and TIGRRepeats), CDS then gene features (i.e. introns and UTRs) from Oryza sativa ssp japonica var Nipponbare MSU v7.0 annotation, and finally the MSU v7.0 rice genome for th […]

library_books

Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

2016
BMC Plant Biol
PMCID: 4736629
PMID: 26833063
DOI: 10.1186/s12870-016-0725-4

[…] 1e-05 and covering at least 80 aa of the query sequence were retained. Paralog sequences from the most abundant and representative LTR-RTs identified in rice and maize were retrieved from Repbase [], RetrOryza [] and MaizeTEDB (http://maizetedb.org/~maize/) and added to the teff dataset. All the paralogs were then aligned separately for each TE class using Muscle []. The multiple alignments were t […]

library_books

Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

2011
PLoS One
PMCID: 3053390
PMID: 21423767
DOI: 10.1371/journal.pone.0017726

[…] (TEs) were first identified and annotated by RepeatMasker searches (http://www.repeatmasker.org) against local databases of rice TEs downloaded from the REPBASE , from the TIGR repeat database , and RetrOryza , and finally manually corrected. De novo prediction of TEs was performed according to structure of the different classes of TEs. The final annotation of the BAC sequences was performed usin […]

call_split

An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

2010
PLoS One
PMCID: 2956642
PMID: 20976139
DOI: 10.1371/journal.pone.0013461
call_split See protocol

[…] a cutoff of 1e-21. BAC end sequences (BES) in this physical map were masked with RepeatMasker v 3.2.7 , using a custom database which integrates repeats from Repbase and plant repeat databases and RetrOryza . Masked BES were aligned to the supercontigs equal or larger than 1 Mb from the Brachypodium sequence draft with BLAT. The physical map, BLAT output files and the largest 17 supercontigs (r […]

library_books

Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

2008
BMC Plant Biol
PMCID: 2607281
PMID: 19055717
DOI: 10.1186/1471-2229-8-123

[…] DataBase assemblies []. Only perfect matches were considered. To identify sequences matching on transposable elements, each locus was mapped on the Rice Annotation Project DataBase assemblies [] and RetrOryza database []. Sequences co-localising with transposable elements were discarded. We then searched for a potential miRNA* sequence using WU-BLAST [] with a maximum distance of 800 bp and a min […]

call_split

Characterization of the major fragance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice

2008
PMCID: 2470208
PMID: 18491070
DOI: 10.1007/s00122-008-0780-9
call_split See protocol

[…] able through the RiceGAAS website (http://ricegaas.dna.affrc.go.jp). Transposable elements (TEs) were identified using RepeatMasker (http://www.repeatmasker.org) with the TIGR Repeat database and the RetrOryza database (Chaparro et al. ) (http://www.retroryza.org). Final annotation was performed using the Artemis annotation tool (Rutherford et al. ). Comparative sequence analyses were performed by […]

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RetrOryza institution(s)
Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-Université de Perpignan, Perpignan, France; Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
RetrOryza funding source(s)
This work was supported by the ITEGE project (ANR-05-BLAN-0244-03) and both ANR and CNRS.

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