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Protocols

Gramene specifications

Information


Unique identifier OMICS_02700
Name Gramene
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Oryza sativa

Documentation


Maintainer


  • person_outline Doreen Ware

Additional information


http://ensembl.gramene.org/info/website/index.html

Publications for Gramene

Gramene citations

 (230)
library_books

A deeper view into the significance of simple sequence repeats in pre miRNAs provides clues for its possible roles in determining the function of microRNAs

2018
BMC Genet
PMCID: 5941480
PMID: 29739315
DOI: 10.1186/s12863-018-0615-x

[…] e.org). Among the miRNA precursors of the same genus but different species, the species with more number of miRNAs were included. Simple Sequence Repeat Identification Tool (SSRIT) [] (http://archive.gramene.org/db/markers/ssrtool markers/ssrtool) was used to study the frequency, type and distribution pattern of SSRs in each individual sequences.To identify the presence of different functional RNA […]

library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] ghth of total sequenced angiosperms.Many of these comprehensive genome databases are well-maintained and are frequently updated with release of new versions, such as PlantGDB V187, Phytozome V12, and Gramene V36. Phytozome updates roughly each year, and PGDD and CoGe update timely upon availability of new genome data. Another feature is that these databases are empowered with various tools other t […]

library_books

Genome wide identification of wheat (Triticum aestivum) expansins and expansin expression analysis in cold tolerant and cold sensitive wheat cultivars

2018
PLoS One
PMCID: 5875846
PMID: 29596529
DOI: 10.1371/journal.pone.0195138

[…] The sequences of the 18 identified previously TaEXP genes [] were used to identify new TaEXPs using a blastn search against the Triticum aestivum genome sequences from GRAMENE (http://ensembl.gramene.org/) []. Sequences of Triticum urartu expansin genes [] were also used to further identify TaEXPs in Triticum aestivum by BLAST against the IWGSC database. In addition […]

library_books

Cross species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species

2018
PLoS One
PMCID: 5873934
PMID: 29590108
DOI: 10.1371/journal.pone.0192678

[…] larger number of both shared drought responsive genes among all species and that of sorghum specific based on sequence similarity search using expression data () than based on querying known genes in Gramene database () suggests the presence of new biological information content in the expression dataset. […]

library_books

Mutation in Rice Abscisic Acid2 Results in Cell Death, Enhanced Disease Resistance, Altered Seed Dormancy and Development

2018
Front Plant Sci
PMCID: 5882781
PMID: 29643863
DOI: 10.3389/fpls.2018.00405

[…] tant and the WT DNA pools, respectively. The physical linkage map was then constructed using molecular markers nearby the lmm9150 gene.The SSR primers were synthesized according to the information of Gramene database. InDel markers were developed based on the alignment results of the reference 93–11, an indica rice and the Nipponbare, a japonica rice2 genome sequence at the candidate region. Prime […]

library_books

The vesicle trafficking regulator PN_SCD1 is demethylated and overexpressed in florets of apomictic Paspalum notatum genotypes

2018
Sci Rep
PMCID: 5812994
PMID: 29445151
DOI: 10.1038/s41598-018-21220-4

[…] cnología de Rosario, Argentina) using TRINOTATE (https://trinotate.github.io/). In silico mapping predictions were conducted by doing BLASTN searches onto the Oryza sativa subsp. Indica genome at the Gramene website (www.gramene.org). For 454/Roche comparative quantitation, we used the data originated from mapping the reads originated from each 454 library (apo or sex) onto a global (apo + sex) as […]

Citations

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Gramene institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA; Division of Biological Sciences and Institute for Basic Science, Wonkwang University, Iksan, Korea; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK; Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY, USA; Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, Canada; Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto, Canada; American Society of Plant Biologists, Rockville, MD, USA; USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, USA
Gramene funding source(s)
Supported by National Science Foundation [IOS-1127112]; United States Department of Agriculture––Agricultural Research Service [58-1907-4-030 and 8062-21000-041-00D]; United Kingdom Biotechnology and Biosciences Research Council [B/I008071/1, BB/J00328X/1, BB/P016855/1], the Reactome database project via a grant from the US National Institutes of Health [U41 HG003751], EU grant [LSHG-CT-2005–518254]; ‘ENFIN’, the Ontario Research Fund; EBI Industry Programme and Oregon State University (OSU).

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