See also legacy data in the Gramene's Archive.
Species | Assembly | Gene Annotation | |
---|---|---|---|
Unchanged | |||
Aegilops tauschii | ASM34733v1 | GCA_000347335.1 | |
Amborella trichopoda | GCA_000471905.1 (AMTR1.0) | 2014-01-AGD | |
Arabidopsis lyrata | Araly1.0 | Araly1.0 | |
Arabidopsis thaliana | TAIR10 | TAIR10 | |
Brachypodium distachyon | Brachy1.0 | Barchy1.2 | |
Brassica oleracea | GCA_000092065.1 | ENA | |
Brassica rapa | IVFCAASv1 | bra_v1.01_SP2010_01 | |
Chlamydomonas reinhardtii | v3.0 | 2007-11-ENA | |
Cyanidioschyzon merolae | 2008-11-ENA | ASM9120v1 | |
Glycine max (soybean) | Glyma1.0 | Glyma1.1 | |
Hordeum vulgare (barley) | 030312v2 | IBSC_1.0 | |
Leersia perrieri | GCA_000325765.3 | OGE | |
Medicago truncatula | MedtrA17_3.5 | 2011-11-EnsemblPlants | |
Musa acuminata (banana) | MA1 | 2012-08-Cirad | |
Oryza barthii | GCA_000182155.1 | OGE Maker (Aug 2013) | |
Oryza brachyantha | GCA_000231095.2 / OGEv1.4b | OGEv1.4 | |
Oryza glaberrima | GCA_000147395.1 / AGI1.1 (May 2011) | 2011-05-AGI (MIPS) | |
Oryza glumaepatula | GCA_000576495.1 | OGE Maker (Aug 2013) | |
Oryza longistaminata | v0117-2013Aug | OGE | |
Oryza meridionalis | GCA_000338895.1 | OGE Maker (Aug 2013) | |
Oryza nivara | GCA_000576065.1 | OGE Maker (Aug 2013) | |
Oryza punctata | GCA_000573905.1 | OGE Maker (Aug 2013) | |
Oryza rufipogon | PRJEB4137 | OGE | |
Oryza sativa japonica | IRGSP-1.0 | MSU 7.0 | |
Oryza sativa indica | ASM465v1 | 2010-07-BGI | |
Ostreococcus lucimarinus | v2.0 GCA_000092065.1 | JGI | |
Physcomitrella patens | ASM242v1 | 2011-03-Phypa1.6 | |
Prunus persica | Prupe1_0 / GCA_000346465.1 | Prupe1_0 / Peach v1.0 | |
Populus trichocarpa | JGI 2.0 | 2010-01-JGI | |
Selaginella moellendorffii | v1.0 | 2011-05-ENA | |
Setaria italica (foxtail millet) | JGIv2.0 | JGIv2.1 | |
Solanum lycopersicum (tomato) | SL2.50 | ITAG2.3 | |
Solanum tuberosum (potato) | 3.0 | SolTub_3.0 | |
Sorghum bicolor | Sorbi1 | 2007-12-JGI | |
Theobroma cacao (cocoa) | GCA_000403535.1 | ENA | |
Triticum aestivum | IWGSP1 | IWGSP1 (MIPS) | |
Triticum urartu | GCA_000347455.1 | GCA_000347455.1 (ENA, Apr 2013) | |
Vitis vinifera | IGGP 12x | 2012-07-CRIBI | |
Zea mays (corn) | B73_RefGen_v3 | 5b+ |
Unchanged | Arabidopsis thaliana |
---|---|
Brachypodium sylvaticum | |
Oryza glaberrima | |
Oryza sativa | |
Solanum lycopersicum | |
Sorghum bicolor | |
Triticum aestivum | |
Vitis vinifera | |
Zea mays |
The EnsemblCompara GeneTree database was not updated in this release. Last update was done in release 46 (June 2015).
The OGE Compara tree was not updated at oge.gramene.org. Last update was done in release 38 (August 2013). Note: The OGE Compara tree was pulled out from the website since they were build on the obsolete MSU6 genome assembly.
Split gene predictions were not updated in this release. Last update was done in release 45 (April 2015). See summary statistics in release 45 and Gramene's FTP site.
No new synteny data was generated for this release. Last update was done in release 39 (October 2013).
Whole genome alignments were not updated in this release. Last update was done in release 46 (June 2015).
UniProtKB cross-references were not updated in this release. Last update was done in release 46 (June 2015).
No new data in the Plant Gene and Plant Variation Marts in this release. Data was last updated in release 46 (June 2015).
Summary tables for the Cyc pathway databases created by Gramene can be seen in release 46 notes.
The Plant Reactome web site (http://plantreactome.gramene.org) is now running version 3 of the Reactome software platform. Notable new features include:
Data analysis tools
Diagram overlay visualization of gene lists, Uniprot IDs, compound identifiers, and/or -omics expression data
Inter-species pathway comparison
Advanced search features built on the Apache Solr platform
RESTful API for programmatic access to Plant Reactome data
Redesigned Pathway Browser user interface
Updated web site design built on Wordpress
Projection Statistics
The latest (projection statistics)[http://plantreactome.gramene.org/stats.html] are available from the Plant Reactome website.
No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.
Gramene's web services page documents many ways to directly connect to and analyze our databases.
Programmatic access to Gramene is now available through the RESTful Ensembl API.
Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following:
mysql -hgramenedb.gramene.org -pgramene