Although we have a new look, you can still find all the old stuff at Gramene's Archive.
Species | Assembly | Gene Annotation | |
---|---|---|---|
New | |||
Amborella trichopoda | GCA_000471905.1 (AMTR1.0) | 2014-01-AGD | |
Prunus persica | Prupe1_0 / GCA_000346465.1 | Prupe1_0 / Peach v1.0 | |
Oryza meridionalis | GCA_000338895.1 | OGE Maker (Aug 2013) | |
Oryza glumaepatula | GCA_000576495.1 | OGE Maker (Aug 2013) | |
Oryza nivara | GCA_000576065.1 | OGE Maker (Aug 2013) | |
Updated | |||
Triticum aestivum | IWGSP1 | IWGSP1 (MIPS) | |
Oryza barthii | GCA_000182155.1 | OGE Maker (Aug 2013) | |
Oryza punctata | GCA_000573905.1 | OGE Maker (Aug 2013) | |
Unchanged | |||
Aegilops tauschii | ASM34733v1 | GCA_000347335.1 | |
Arabidopsis lyrata | Araly1.0 | Araly1.0 | |
Arabidopsis thaliana | TAIR10 | TAIR10 | |
Brachypodium distachyon | Brachy1.0 | Barchy1.2 | |
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 | |
Medicago truncatula | MedtrA17_3.5 | 2011-11-EnsemblPlants | |
Musa acuminata (banana) | MA1 | 2012-08-Cirad | |
Oryza brachyantha | GCA_000231095.2 / OGEv1.4b | OGEv1.4 | |
Oryza glaberrima | GCA_000147395.1 / AGI1.1 (May 2011) | 2011-05-AGI (MIPS) | |
Oryza sativa japonica | IRGSP-1.0 | MSU 7.0 | |
Oryza sativa indica | ASM465v1 | 2010-07-BGI | |
Physcomitrella patens | ASM242v1 | 2011-03-Phypa1.6 | |
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) | SL2.40 | ITAG2.3 | |
Solanum tuberosum (potato) | 3.0 | SolTub_3.0 | |
Sorghum bicolor | Sorbi1 | 2007-12-JGI | |
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+ | |
Leersia perrieri (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
Oryza granulata (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
Oryza longistaminata (chr3s) | OGE.2012Jul | 2012-10-CSHL | |
Oryza minuta (BB) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
Oryza minuta (CC) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
Oryza officinallis (CC) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
Oryza rufipogon (AA) chr3s | 454.pools.1.1 (Jul 2010) | CSHL | |
Oryza rufipogon (AA) FPC | OMAP_FPC_2006_JAN |
Updated | Sorghum bicolor |
---|
Unchanged | Arabidopsis thaliana |
---|---|
Brachypodium sylvaticum | |
Hordeum vulgare | |
Oryza glaberrima | |
Oryza sativa | |
Triticum aestivum | |
Vitis vinifera | |
Zea mays |
The OGE Compara tree was not updated. 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.
Potential gene annotation artifacts
Split gene analysis was done for the 33 fully sequenced plant reference genomes in Gramene release 41. This analysis includes information on 10 new genomes, compared to the last split gene split done in release 38. For a complete list, see Gramene's FTP site. Summary statistics follow.
Split genes by species
Species | Count |
---|---|
Aegilops tauschii | 534 |
Amborella trichopoda | 739 |
Arabidopsis lyrata subsp. lyrata | 81 |
Arabidopsis thaliana | 21 |
Brachypodium distachyon | 108 |
Brassica rapa subsp. pekinensis | 107 |
Chlamydomonas reinhardtii | 45 |
Cyanidioschyzon merolae | 4 |
Glycine max | 254 |
Hordeum vulgare subsp. vulgare | 65 |
Medicago truncatula | 285 |
Musa acuminata | 1134 |
Oryza barthi | 147 |
Oryza brachyantha | 198 |
Oryza glaberrima | 357 |
Oryza glumaepatula | 206 |
Oryza meridionalis | 125 |
Oryza nivara | 117 |
Oryza punctata | 151 |
Oryza sativa Indica Group | 509 |
Oryza sativa Japonica Group | 398 |
Physcomitrella patens subsp. patens | 173 |
Populus trichocarpa | 1196 |
Prunus persica | 276 |
Selaginella moellendorffii | 70 |
Setaria italica | 171 |
Solanum lycopersicum | 784 |
Solanum tuberosum | 412 |
Sorghum bicolor | 607 |
Triticum aestivum | 772 |
Triticum urartu | 447 |
Vitis vinifera | 440 |
Zea mays | 564 |
No new synteny data was generated for this release. Last update was done in release 39 (October 2013).
DNA-DNA alignments between bread wheat and Oryza sativa, bread wheat and Brachypodium distachyon, and barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii).
RNA-Seq data aligned to bread wheat, as well as to its wild progenitors.
Wheat UniGene clusters sequences aligned to bread wheat, as well as to its wild progenitors.
No updates in this release. Last update done in release 40 (January 2014).
New Plant Gene and Plant Variation Marts
Class | Pathway name |
---|---|
Hormones | strigolactone biosynthesis |
Amines and Polyamines | allantoin degradation I |
Inorganic Nutrients Metabolism | sulfate activation for sulfonation |
thiosulfate disproportionation III (rhodanese) | |
ammonia assimilation cycle |
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No updates in this release. Last update done in release 31 (May 2010). Below is a summary of the ontologies data.
Prefix | Term Type | Count |
---|---|---|
EO | plant_environment_ontology | 500 |
GO | biological_process | 24767 |
GO | cellular_component | 3194 |
GO | molecular_function | 10376 |
GRO | cereal_plant_growth_stage | 235 |
GR_tax | gramene_taxonomy | 58550 |
PO | plant_anatomy | 1295 |
PO | plant_structure_development_stage | 324 |
TO | plant_trait_ontology | 1290 |
See also the detailed Ontology Module statistics report.
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