You'll notice we have a new look. You can find all the old stuff at Gramene's Archive.
Species | Assembly | Gene Annotation | |
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Updated | |||
Oryza sativa japonica | IRGSP-1.0 / MSU 7.0 | IRGSP-1.0 / MSU 7.0 | |
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 barthii | OGE.2012Jul | 2012-10-CSHL | |
Oryza brachyantha | OGEv1.4b | OGEv1.4 | |
Oryza glaberrima | AGI1.1 (May 2011) | 2011-05-AGI | |
Oryza sativa indica | ASM465v1 | 2010-07-BGI | |
Oryza punctata | Mar 2013 | CSHL Mar 2013 | |
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 aestivum | IWGSP1 | IWGSP1 | |
Triticum urartu | ASM34745v1 | GCA_000347455.1 | |
Vitis vinifera | IGGP 12x | 2012-07-CRIBI | |
Zea mays (corn) | B73_RefGen_v3 | 5b+ | |
Leersia perrieri (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
Oryza glumaepatula (chr3s) | 454.pools.2012Feb | 2012-04-CSHL | |
Oryza granulata (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
Oryza longistaminata (chr3s) | OGE.2012Jul | 2012-10-CSHL | |
Oryza meridionalis (chr3s) | 454.pools.2012Feb | 2012-04-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 nivara (AA) chr3s | 454.pools.1.1 (Jul 2010) | CSHL | |
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 |
Unchanged | Arabidopsis thaliana |
---|---|
Brachypodium sylvaticum | |
Hordeum vulgare | |
Oryza glaberrima | |
Oryza sativa | Sorghum bicolor |
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
No new split gene annotations were identified for this release. Last update was done in release 38 (August 2013). For a complete list, see Gramene's FTP site. Summary statistics follow.
Split genes by species
Species | Count |
---|---|
Arabidopsis lyrata subsp. lyrata | 172 |
Arabidopsis thaliana | 34 |
Brachypodium distachyon | 150 |
Brassica rapa subsp. pekinensis | 150 |
Chlamydomonas reinhardtii | 96 |
Cyanidioschyzon merolae | 8 |
Glycine max | 404 |
Hordeum vulgare subsp. vulgare | 56 |
Musa acuminata | 1558 |
Oryza barthi | 1 |
Oryza brachyantha | 334 |
Oryza glaberrima | 436 |
Oryza sativa Indica Group | 730 |
Oryza sativa Japonica Group | 628 |
Physcomitrella patens subsp. patens | 248 |
Populus trichocarpa | 2076 |
Selaginella moellendorffii | 172 |
Setaria italica | 362 |
Solanum lycopersicum | 1138 |
Solanum tuberosum | 648 |
Sorghum bicolor | 1036 |
Vitis vinifera | 876 |
Zea mays | 1160 |
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.
Updated functional domain (InterPro) and ontology (InterPro2GO) annotation.
New Plant Gene and Plant Variation Marts
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MaizeCyc was updated to Version 2.2 with 37 updated GO annotations, evidence codes and publication references.
NOTE: BioPAX level 2 and 3 generated with the pathway tools software have a discrepant number of pathways. For more details, please see the note in the MaizeCyc 2.2 FTP directory.
32 new rice pathways have been added to the Plant Reactome, including the signaling pathway for the plant hormone ethylene. 8 pathways have been updated.
Modified pathways
ABA biosynthesis and signalling pathway |
Calvin cycle |
TCA cycle |
oleoresin sesquiterpene volatiles biosynthesis |
oleoresin monoterpene volatiles biosynthesis |
carotenoid biosynthesis |
monoterpene biosynthesis |
polyisoprenoid biosynthesis |
New pathways
Ethylene biosynthesis and signaling |
Oryzalexin S biosynthesis |
S-adenosyl-L-methionine cycle |
S-methylmethionine cycle |
UDP-L-arabinose biosynthesis I |
UDP-L-arabinose biosynthesis II |
alanine biosynthesis II |
alanine biosynthesis III |
arginine biosynthesis I |
arginine biosynthesis II |
aspartate biosynthesis I |
beta-alanine biosynthesis I |
beta-alanine biosynthesis III |
cysteine biosynthesis I |
fructan biosynthesis |
fructan degradation |
galactose degradation II |
geranylgeranyl diphosphate biosynthesis II |
histidine biosynthesis I |
methionine biosynthesis II |
methionine salvage pathway |
mevalonate pathway |
momilactone biosynthesis |
oryzalexin A-F biosynthesis |
phytyl-pp biosynthesis |
putrescine biosynthesis I |
putrescine biosynthesis II |
putrescine biosynthesis III |
spermidine biosynthesis |
spermine biosynthesis |
sucrose biosynthesis |
tetrapyrrole biosynthesis I |
No updates in this release (except for updated InterPro2GO annotations under 'Protein Annotation, Go, Xref' section above). 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