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Release Notes
Release Notes
Version 28 - September 2008
The Mart database will be available shortly after the main release. Estimated delivery is October 1, 2008.
No new maps were added for this release. However, all maps were updated, where necessary, based on updated data from the Markers Module. To decrease display time, the number of features dumped to CMap has been significantly reduced for two rice sequence maps and two maize physical maps. Additionally, CMap has been upgraded to the latest released version (1.01).
See also the detailed Map Module statistics report.
For release 28, the markers database contains a total of 43,727,655 markers. New markers of note are the Microarray Probes, which includes sequence data from rice DNA microarrays, including arrays from Affymetrix, Agilent, and NSF. Sequences (ESTs, GSSs, etc.) have been updated based on data in Genbank as of 2008-07-14. SSRs have a new sequence display that highlights the primer sequence in green and the repeat motif in red (e.g., RM426).
Marker breakdown by type
|
Marker breakdown by species
|
See also the more detailed Marker Module statistics report.
The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.
Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.
| Ontology | Total terms | Total Terms w/Associations | Total Associations |
| Gene Ontology (GO) | 26546 |
2217 |
414936 |
| Plant Ontology (PO) | 855 |
174 |
17052 |
| Growth stage Ontology (GRO) | 236 |
62 |
14676 |
| Trait Ontology (TO) | 973 |
491 |
14032 |
| Taxonomy Ontology (GR_tax) | 58172 | 3259 |
191465 |
| Environment Ontology (EO) | 496 |
69 |
12105 |
Content: Number of genes
Improvements include:
A more detailed genes database statistics report can be found here.
| Rice | 8,646 |
| Maize | 1,747 |
| Oat | 375 |
| Barley | 299 |
| Pearl millet | 284 |
| Sorghum | 136 |
| Foxtail millet | 65 |
| Wild rice | 41 |
| Wheat | 23 |
| Tetraploid wheat | 8 |
| Total | 11,624 |
One recent change is the improvement of search and display interface.A user can now search QTLs via their associated genes, annotated PO terms (plant structure or plant growth stages, environmental conditions) and markers. In addition, we include the associated markers in QTL search summary page and download. The enhanced query capacity and download function will greatly facilitate gene discovery as well as marker-assisted selection.
A more detailed QTL database statistics report can be found here.
This release includes Updated RiceCyc (v 2.0.2.1), AraCyc mirror (v 4.5), Ecocyc mirror (v 12.0) and MetaCyc (v 12.0). The database is served by the Pathway Tools version 12.0, that is develoed by the SRI International. The pathway databases on SorghumCyc, MedicCyc, LycoCyc, CapCyc, PotatoCyc, CoffeaCyc have not changed in this release.
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in rice (Oryza sativa).
RiceCyc now allows you to draw comparisons among the data sets from eight
species.
2 pathways on Iron uptake were added, All the pathways changes are
recorded here
This tool also allows you to upload your own gene
expression data on the pathways to visualise an overview
of the cellular level expression profile.
For more information please visit RiceCyc start page.
The Gramene Genetic Diversity database contains phenotype, SSR, RFLP, and AFLP allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
On this release: Diversity Release Notes (Build 28, 9/20/2008)
The Gramene Genetic Diversity database contains phenotype, SNP, SSR and RFLP allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
On this release:
Click here for database summary.
Version 27 - April 2008
NULL:not tried to load into ensembl db
Genome breakdown
| track_name | Arabidopsis thaliana TAIR7 | BGI 93-11 Sequence 2005 | Gramene Annotated Nipponbare Sequence 2006 | Oryza glaberrima | Populus trichocarpa JGI 2004 | Sorghum bicolor JGI8X 2007 | vitis vinifera iggp2007 |
| African-rice_EST | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| African-rice_mRNA | 3 | 33 | 36 | 0 | 6 | 28 | 12 |
| American-cotton_EST | NULL | NULL | NULL | NULL | NULL | NULL | 222239 |
| American-cotton_mRNA | NULL | NULL | NULL | NULL | NULL | NULL | 1984 |
| Chinese-cabbage_EST | 473236 | NULL | NULL | NULL | NULL | NULL | NULL |
| Chinese-cabbage_mRNA | 873 | NULL | NULL | NULL | NULL | NULL | NULL |
| Indian-rice_EST | 86554 | 401716 | 241334 | 130342 | 101447 | 347168 | 98719 |
| Indian-rice_mRNA | 4562 | 36118 | 28961 | 8458 | 6085 | 35194 | 6410 |
| Japanese-rice_EST | 244999 | 1736617 | 1533230 | 387429 | 325851 | 1379345 | 307253 |
| Japanese-rice_mRNA | 46724 | 478852 | 366952 | 94908 | 66958 | 462736 | 68026 |
| MEDICAGO-TRUNCATULA_EST | NULL | NULL | NULL | NULL | 297894 | NULL | NULL |
| MEDICAGO-TRUNCATULA_mRNA | NULL | NULL | NULL | NULL | 1751 | NULL | NULL |
| Maize_EST | 340484 | 1938676 | 1257619 | 348984 | 395772 | 2541766 | 378598 |
| Maize_mRNA | 14768 | 77891 | 92894 | 13702 | 17503 | 90395 | 16014 |
| ORYZA-MINUTA_EST | NULL | 11049 | 11007 | NULL | NULL | NULL | NULL |
| ORYZA-MINUTA_mRNA | NULL | 29 | 20 | NULL | NULL | NULL | NULL |
| Porteresia-coarctata_EST | NULL | 211 | 175 | NULL | NULL | NULL | NULL |
| Porteresia-coarctata_mRNA | NULL | 20 | 25 | NULL | NULL | NULL | NULL |
| Rice_EST | NULL | 276377 | 339150 | NULL | NULL | 214671 | NULL |
| Rice_mRNA | NULL | 6214 | 4437 | NULL | NULL | 6778 | NULL |
| Sorghum_EST | 82072 | 469012 | 323895 | 76705 | 99752 | 491145 | 101239 |
| Sorghum_mRNA | 985 | 8467 | 5976 | 82 | 1379 | 10839 | 1328 |
| Wheat_EST | 643579 | 2449623 | 1723307 | 399465 | 693084 | 2249104 | 641461 |
| Wheat_mRNA | 3031 | 15666 | 12710 | 3198 | 3744 | 15136 | 3113 |
| apple_EST | 185614 | NULL | NULL | NULL | 351220 | NULL | 305495 |
| apple_mRNA | 708 | NULL | NULL | NULL | 1544 | NULL | 1310 |
| black-cottonwood_EST | 74086 | 39836 | 39973 | 19386 | 229512 | 36888 | 125251 |
| black-cottonwood_mRNA | 460 | 192 | 205 | 23 | 1350 | 150 | 729 |
| cultivated-barley_EST | 186901 | 773711 | 507915 | 127160 | NULL | 718177 | 207426 |
| cultivated-barley_mRNA | 4876 | 33411 | 3725 | 5150 | NULL | 30717 | 5630 |
| noble-cane_EST | NULL | 589683 | 425508 | 92494 | NULL | 718487 | NULL |
| noble-cane_mRNA | NULL | 1543 | 1209 | 269 | NULL | 1330 | NULL |
| oilseed-rape_EST | 1326584 | NULL | NULL | 118524 | 493856 | NULL | NULL |
| oilseed-rape_mRNA | 3975 | NULL | NULL | 148 | 1442 | NULL | NULL |
| potatoes_EST | NULL | NULL | NULL | NULL | NULL | NULL | 219112 |
| potatoes_mRNA | NULL | NULL | NULL | NULL | NULL | NULL | 3313 |
| soybeans_EST | 233240 | NULL | NULL | NULL | 445881 | NULL | 281747 |
| soybeans_mRNA | 2579 | NULL | NULL | NULL | 5562 | NULL | 3868 |
| thale-cress_EST | 2075040 | 238725 | 224148 | 93984 | 471171 | 234612 | 340373 |
| thale-cress_mRNA | 362705 | 29539 | 29395 | 6166 | 123021 | 28633 | 67919 |
| wine-grape_EST | 285302 | 249934 | 232562 | 101107 | 610750 | 225427 | 823338 |
| wine-grape_mRNA | 748 | 595 | 609 | 118 | 2307 | 620 | 2025 |
See also the detailed Map Module statistics report.
For release 27, the markers database contains a total of 30,216,904 markers. The database includes up-to-date nucleotide sequences of all Viridiplantae contained in the NCBI Genbank Core Nucleotide, dbEST, and dbGSS divisions. We have also new and updated EST Cluster records from NCBI UniGene, PlantGDB PUT, and Plant Gene Indices.
Markers breakdown
Marker breakdown by type
|
Marker breakdown by major species
|
See also the more detailed Marker Module statistics report.
The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.
NEW: For the first time we have introduced a Gazetteer (GAZ) in the Gramene project. GAZ is developed by a group of experts and researchers including those from Gramene database. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles (controlled vocabulary), that describes places and place names and the relations between them. In Gramene databse we have used GAZ in the Diversity database to annotate the source site of germplasm colelction.
UPDATED: Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.
Ontology breakdown
| Ontology | Total terms | Total Terms w/Associations | Total Associations |
| Gene Ontology (GO) | 26143 |
3523 |
441666 |
| Plant Ontology (PO) | 853 |
165 |
16911 |
| Growth stage Ontology (GRO) | 236 |
94 |
17560 |
| Trait Ontology (TO) | 973 |
486 |
13989 |
| Taxonomy Ontology (GR_tax) | 3259 | 3237 |
190486 |
| Environment Ontology (EO) | 496 |
67 |
12074 |
| Gazetteer Ontology (GAZ) | 78214 |
90 |
728 |
Content: Number of genes
A more detailed genes database statistics report can be found here.
Number of QTLs
A more detailed QTL database statistics report can be found here.
Pathways section in the Gramene databases is the home for RiceCyc and SorghumCyc. It also provides mirrors of the MetaCyc based compilation of metabolic pathway databases from seven other species and the reference database MetaCyc listed below. The database provides a curated and predicted catalog of biochemical pathways from 8 species, allows users to find the species specific genes mapped to respective pathways and draw comparisons between the pathways.
Pathways breakdown
| Database | Species | Version | Source |
| RiceCyc # | Oryza sativa japonica cv. Nipponbare | 2.0 | Gramene database |
| SorghumCyc # | Sorghum bicolor cv. BTx623 | 1.0 beta | Gramene database & Sorghum Biomass/Feedstock project |
| AraCyc* | Arabidopsis thaliana strain Columbia | 4.1 | The Arabidopsis Information Resource (TAIR) |
| MedicCyc* | Medicago truncatula, Barrelclover | 1.0.1 | The SR Noble Foundation |
| LycoCyc* | Solanum lycopersicum, Tomato | 1.0.1 | Solanaceae Genomics Network (SGN) |
| CapCyc* | Capsicum annuum, Pepper | 1.0.1 | Solanaceae Genomics Network (SGN) |
| CoffeeCyc* | Coffea canephora, Coffee | 1.0.1 | Solanaceae Genomics Network (SGN) |
| PotatoCyc* | Solanum tuberosum, Potato | 1.0.1 | Solanaceae Genomics Network (SGN) |
| EcoCyc* | Escherichia coli strain K-12 MG1655 | 11 | SRI International |
| MetaCyc* | Reference pathways | 11 | SRI International |
NEW:
SorghumCyc rel 1.0 beta is released for the first time. It is based on Sorghum bicolor cv BTx623 genome assembly v1.4 of the JGI
RiceCyc ver 2.0 is based on the TIGR pseudomolecule assembly release 5 of the IRGSP finished sequence. 83 pathways have been added of which 4 phytoalexin biosynthesis pathways were added manually [e.g. momilactone biosynthesis, oryzalexin A-F biosynthesis, oryzalexin S biosynthesis, phytocassane biosynthesis].
Users are also allowed to upload the gene expression/proteomics/metabolomics data on the pathways to visualise an overview of the cellular level expression profile.
For more information please visit Pathway section.
The Gramene Genetic Diversity database contains phenotype and genotype allelic data for rice, phenotype and genotype data for maize, SNP data for wheat, and Sequencing and SSR data for sorghum. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
This is the first time for Gramene to have the sorghum diversity data. The most sorghum data are currently contributed by the Institute for Genomic Diversity (IGD), Cornell University.
For the first time rice germplasms are annotated with Gazetteer ontology (GAZ). For more information, please see Ontology section of release notes.
On this release:
Click here for database summary.
Version 26 - September 2007
The help documentation has also been put into this consistent interface with expandable/collapsible sections. You may view it at http://dev.gramene.org/db/help
| Rice_mRNA: | 6048 |
| Maize_mRNA: | 3 |
| Other-poaceae_mRNA: | 433 |
| Rice_est: | 1 |
| Maize_est: | 156 |
| Wheat_est: | 75 |
| Other-poaceae_est: | 384 |
| RiceAlta_BACend_OMAP: | 162517 |
| RiceOfficinalis_BACend_OMAP: | 164407 |
| RiceBrachyantha_BACend_OMAP: | 74492 |
| RiceMinuta_BACend_OMAP: | 246173 |
| RiceGlaberrima_BACend_OMAP: | 106083 |
| RiceCoarctata_BACend_OMAP: | 152773 |
| RiceRufipogon_BACend_OMAP: | 165183 |
| RiceGranulata_BACend_OMAP: | 133152 |
| RicePunctata_BACend_OMAP: | 114588 |
| RiceNivara_BACend_OMAP: | 257131 |
| RiceAustraliensis_BACend_OMAP: | 185298 |
Data in the Maps Module is built out of the mappings in the Markers Module. Updates in the latter module are also reflected here. Of note is the new sequence map for indica. As noted in the "Genomes" section above, the OMAP sets have all been updated.
See also the detailed Map Module statistics report.
For release 26, the markers database contains a total of 13,504,402 markers. New markers of note are 2,243 maize eSSRs from the Maize Genome Sequencing Project.
Marker breakdown by type
|
Marker breakdown by species
|
See also the more detailed Marker Module statistics report.
The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.
Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.
| Ontology | Total terms | Total Terms w/Associations | Total Associations |
| Gene Ontology (GO) | 24936 |
3585 |
455272 |
| Plant Ontology (PO) | 834 |
158 |
16057 |
| Growth stage Ontology (GRO) | 236 |
91 |
16118 |
| Trait Ontology (TO) | 834 |
484 |
13846 |
| Taxonomy Ontology (GR_tax) | 2699 | 1419 |
185279 |
| Environment Ontology (EO) | 497 |
56 |
596 |
Content: Number of genes
Improvements include:
A more detailed genes database statistics report can be found here.
Number of QTLs
One recent improvement is that all QTL have been described and annotated by multiple ontologies. In addition to Trait Ontology (TO and Plant Ontology (PO) terms used in previous releases, Environment Ontology (EO) terms have been added this build to describe environmental conditions under which a particular QTL has been identified. These terms have been annotated by creating a default mapping based on the expertly identified TO and EO associations.
Another recent important improvement in this release is the provision of QTL associated molecular marker info. We currently provide two types of associated markers for a particular QTL: Co-localized markers are the markers co-localized or overlapped with a QTL region on the original QTL map, and neighboring markers are those not overlapped but closely adjacent to a QTL region. The associated marker info is crucial for QTL fine mapping, map-based positional cloning, and marker-assisted selection (MAS) for plant breeding.
A more detailed QTL database statistics report can be found here.
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in rice (Oryza sativa).
We are pleased to announce the addition of five new species to the Gramene pathway tools (RiceCyc) module. These are Capsicum anuum, Coffea canephora, Medicago truncatula, Solanum lycopersicum and Solanum tuberosum. Taken together with the previously available Arabidopsis thaliana and bacteria E. coli datasets, RiceCyc now allows you to draw comparisons among the data sets from eight species.
Six pathways have been added, two pathways deleted and five pathways modified during this round of curation. All the pathways changes are recorded here
This tool also allows you to upload your own gene expression data on the pathways to visualise an overview of the cellular level expression profile.
For more information please visit RiceCyc start page.
The Gramene Genetic Diversity database contains phenotype, SSR, RFLP, and AFLP allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
On this release:
Click here for database summary.
Version 25 - June 2007
Gramene Release 25 June 2007
This release includes:.
Gramene website features:
- Quick Search - The search box at the top of every Gramene page has been upgraded to a new search so that results are now faster. You may select a single module to search, or search the entire site. For consistency, this search has been put in the same location on the home page, and the Database Version number has been moved to the upper left column below the navigation bar. For more information, read the help document. For more in-depth module searches, you should still use the module specific searches on their pages (such as maps, markers, genes, etc.)
- New FAQ format - the New FAQ format is quicker to navigate and is much less cluttered. There is now a quick search for searching only the FAQ.
- Did you ever want to better understand where the data in Gramene comes from? The Gramene Collaborators page has been updated with more descriptive explanations of each project's contributions to Gramene. Links to sources and references are supplied as they have been provided are available on the more in-depth page.
Gramene Database:
- Genomes: (See More info)
- Maps: (See More info)
- Markers: (See More info)
- Proteins: (See More info)
- Ontologies: (See More info)
- Genes: (See More info)
- QTL: (See More info)
- Pathways: (See More info)
- Diversity: (See More info)
Genomes Release Notes
New Genomes Data
- Rice Gene Annotation updated to TIGR Rice(Oryza sativa ssp. japonica) Genome Annotation - Release 5. In this release, Gene model structure has been improved for 33,882 gene models (28,706 genes) with ~ 1.2 million of EST and/or full length cDNA evidence using the TIGR PASA program. A portion of models has been manually curated using the expression evidence and comparative genomics studies.
TIGR5 Genes: 57923 TIGR5 Transcripts: 68388
- 230 curated miRNA genes
- Rice QTLs have been updated with 6293 Rice QTLs mapped to rice pseudomolecules
- Mapping of new poaceae EST/mRNA/GSS dna sequences downloaded from NCBI genbank to Oryza sativa TIGR v5 assembly with blat, the succesfully mapped sequences can be viewed as dna align features at contigview. The counts of added align features per track are
Rice_mRNA: 272 Maize_mRNA: 148 Other-poaceae_mRNA: 592 Rice_est: 424 Maize_est: 40 Sorghum_est: 15 Barley_est: 25 Wheat_est: 364772 Other-poaceae_est: 887 RiceJaponica_BACend_OMAP: 638 RiceRufipogon_BACend_OMAP: 54938
- The whole genome alignment comparative analyses were done for Oryza sativa ssp. japonica and Arabidopsis thaliana using both Translated Blat and Blastz-chain-net. User can view the alignments from both ContigView and MultiContigView by selecting the Compara Menu on the Detailed View panel
- Gene tree orthologs/paralogs were computed for four plant species (O.sativa (ssp japonica), O.sativa (ssp indica), Arabidopsis, and poplar) and four model metazoan species (human, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae. For example, from 41908 genes on O.sativa (ssp japonica), we identified that;
29901 have orthologs in O.sativa (ssp indica) 18520 have orthologs in Arabidopsis 19684 have orthologs in poplar 5324 have orthologs in Saccharomyces cerevisiae 7175 have orthologs in Caenorhabditis elegans 7449 have orthologs in Drosophila melanogaster 8313 have orthologs in human
Maps Release Notes
Data in the Maps Module is built out of the mappings in the Markers Module. Updates in the latter module are also reflected here. Of note is the new cytogenetic map of maize from the Cytogenetic Map of Maize project. The gene predictions in the rice genome have been updated to reflect the latest annotations from TIGR release 5.
New maps
- Maize - CMM Cytogenetic FISH 2007
- Rice - USMSU O sativa CL16/O.nivara IRGC 80470 SSR QTL 2006
- Maize - UWM B73/Mo17 RFLP SSR QTL 1996
- Rice - CNNAU IR50/Tatsumimochi/Miyukimochi SSR QTL 2006
Updated gene prediction positions
Updated with new curated QTL
- Rice - UGA BTx623/IS3620C RL SSR RFLP QTL 2006
- Rice - IRRI IR74/Jalmagna RI AFLP/RFLP QTL 2001
- Rice - JUT Akihikari/IRAT109 BC1F4 SSR QTL 2004
See also the detailed Map Module statistics report.
Markers Release Notes
For release 25, the markers database contains a total of 13,952,872 markers. For the sake of clarity, we have changed the name of the marker type "Gene Model" to "Gene Prediction"; these are genes predicted by TIGR on the rice genome. With the addition of the cytogenetic map of maize, a new marker type "FISH probe" has been added.
Marker breakdown by type
Marker Type Markers AFLP 8150 Breakpoint interval 303 Centromere 22 Clone 2605818 deletion 895 EST 4661596 EST Cluster 1325127 FISH probe 31 FPC 22651 Gene 9806 Gene Prediction 96234 Gene Primer 19 GSS 4868955 insertion 686 Maize Bin 114 mRNA 142278 OVERGO 25006 Primer 21482 QTL 11437 RAPD 174 RFLP 17744 SSR 14826 SSR Primer Pair 16883 STS 2234 Unclassified DNA 31524 Undefined 68877 Marker breakdown by species
Species Markers Barley (Hordeum spp.) 682451 Maize (Zea spp.) 4653569 Oat (Avena spp.) 8839 Rice (Oryza spp.) 5124238 Rye (Secale spp.) 13513 Sorghum (Sorghum spp.) 1341868 Sugarcane (Saccharum spp.) 340044 Wheat (Triticum spp. + Aegilops spp.) 1554422 Other 233928 See also the more detailed Marker Module statistics report.
Proteins Release Notes
The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.
- Total number of proteins: 159664
- Proteins from SWISS-PROT: 2631
- Proteins from TrEMBL: 157033
- Proteins with Pfam annotations: 57768
- Proteins with Prosite annotations: 32344
- Proteins with Signal peptide predicted by TargetP: 79933
- Proteins with Transmembrane domains predicted by TMHMM: 32039
- Proteins with Gene Ontology (GO): 101312
- Proteins with Plant Ontology (PO): 179
Ontologies Release Notes
Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.
Ontology Total terms Total Terms w/Associations Total Associations Gene Ontology (GO) 24324 3591 454548 Plant Ontology (PO) 828 151 15924 Growth stage Ontology (GRO) 236 90 16081 Trait Ontology (TO) 829 484 13741 Taxonomy Ontology (GR_tax) 2619 1328 180848 Environment Ontology (EO) 497 50 566
Genes and Alleles Release Notes
Content: Number of genes
- Total -- 9307
- Rice -- 2624 (80 new genes)
- Maize -- 6680
- Sorghum -- 3
Improvements include:
- Most of the rice genes with the first character of the gene symbol from "A" to "S" in our database now have ontology associations to TO, GO and PO.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database now contains a total of 11,437 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.
One important improvement in this release is the provision of QTL associated molecular marker info. We currently provide two types of associated markers for a particular QTL: Co-localized markers are the markers co-localized or overlapped with a QTL region on the original QTL map, and neighboring markers are those not overlapped but closely adjacent to a QTL region. The associated marker info is crucial for QTL fine mapping, map-based positional cloning, and marker-assisted selection (MAS) for plant breeding.
Another improvement in this release is the provision of the inferred rice genome positions for recently curated rice QTL. Together with previous QTL genome positions, currently we provide the inferred positions for more than 6,000 rice QTL. These genome positions are displayed on both Gramene Maps and the Genome Browser, and will greatly enhance users' ability to perform comparative mapping research and candidate gene discovery.
Another recent improvement is that all QTL have been described and annotated by multiple ontologies. In addition to Trait Ontology (TO) terms used in previous releases, Plant Ontology (PO) terms have been added to describe Plant Structure and Plant Growth and Development Stage associated with a particular QTL. These terms have been annotated according to the information from QTL experiments in the cited literature, or by creating a default mapping based on the expertly identified TO and PO associations.
A more detailed QTL database statistics report can be found here.
Pathways Release Notes (version 1.3)
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in plants: rice (Oryza sativa), Arabidopsis thaliana and bacteria E. coli. This tool also allows you to draw comparisons among the data sets from the above three species.
Sixteen pathways have been deleted and fifteen pathways added during this round of curation. All the pathways changes are recorded here
- Pathways: 278
- Enzymatic Reactions: 1687
- Transport Reactions: 5
- Polypeptides: 43172
- Protein Complexes: 4
- Enzymes: 10387
- Compounds: 1265
This tool also allows you to upload your own gene expression data on the pathways to visualise an overview of the cellular level expression profile.
For more information please visit RiceCyc start page.
Diversity Release Notes
The Gramene Genetic Diversity database contains phenotype, SSR and RFLP allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
On this release:
- Rice: 954 germplasm accessions and 672 BC2F1/F2 lines; 782 SSRs and 241 RFLPs; Phenotype data on 21 traits from multi-environment experiments.
- Wheat: 48 germplasm accessions; 3802 SNP markers.
- Maize: 449 germplasm accessions with SNP data; 1544 germplasm accessions with SSR data. 1435 SNP and 520 SSR markers.
- Interface improvement: Now, by clicking the experiment title you can have an overview of all the data, including all the markers and germplasm accessions used, QTLs identified, and phenotype data, available from a study.
Click here for database summary.
Version 24 - March 2007
Gramene Release 24 March 2007
This release includes:.
Gramene website features:
- New species page - Brachypodium
- New newsletter in PDF format, with articles contributed from the research community - Jan/Feb 2007 PDF Newsletter
. Contact the editor to submit articles.Gramene Database:
- Genomes: New repeat tracks. New mapped data added to alignments. (See More info)
- Maps: Built from the Markers module, encorporates changes from markers, as well as several new and updated QTL maps. (See More info)
- Markers: Mostly maintenance was performed. (See More info)
- Proteins: (See More info)
- Ontologies: QTL now associated with ontologies. (See More info)
- Genes: Addition of siRNA genes, and more ontology associations. (See More info)
- QTL: QTL are now annotated by ontologies, and many QTL have links to multiple mapping positions. (See More info)
- Pathways: Many non-rice pathways have been removed. (See More info)
- Diversity: (See More info)
Genomes Release Notes
New Genomes Data
- Repeat features in the rice and Arabidopsis genomes were identified using repeatmasker and the REdat repeat library developed by the Munich Information Center for Protein Sequences (MIPS) [more]. These data have been used to create several new Genome Browser tracks under the 'Repeats' menu;
All repeats
LTRs
RNA repeats
Satellite repeats
Type I Transposons
Type II Transposons
Other/Unknown repeats
- Mapping of the 284 siRNAs reported by Sunkar's group [NAR 2005 Aug 2;33(14):4443-54] to Oryza sativa TIGR v4 assembly with vmatch. 268 succesfully mapped can be viewed as dna align features at contigview (for example, P101-G7), 185 uniquely mapped can also be viewed as genes (for example, P99-H3)
- Mapping of new poaceae EST/mRNA/GSS dna sequences downloaded from NCBI genbank to Oryza sativa TIGR v4 assembly with blat, the succesfully mapped sequences can be viewed as dna align features at contigview. The counts of added align features per track are
Rice_mRNA: 136529 Maize_mRNA: 4461 Other-poaceae_mRNA: 950 Rice_est: 15022 Maize_est: 7975 Other-poaceae_est: 2030 RiceAlta_BACend_OMAP: 124 RiceOfficinalis_BACend_OMAP: 250 RiceMinuta_BACend_OMAP: 478 RiceJaponica_BACend_OMAP: 1392 RiceRufipogon_BACend_OMAP: 279 RiceCoarctata_BACend_OMAP: 51 RiceGranulata_BACend_OMAP: 27 RiceNivara_BACend_OMAP: 75
Maps Release Notes
As with the last release, data in the Maps Module is built out of the mappings in the Markers Module. Updates in the latter module are also reflected here. Of note are two new QTL maps as well as four updated QTL maps upon which new QTL have been added. Pending their curation, OVERGOs on the various OMAP physical maps have not been exported in this build.
New QTL Maps
Updated QTL Maps
- Rice-Aberdeen Bala/Azu QTL 2002
- Barley-Steptoe/Morex DH RFLP QTL 2006
- Barley-Tadmor/Er Apm RI RFLP/AFLP/SSR QTL 1998
- Barley-Apex/H. spontaneum BC SSR QTL 2003
A detailed Map Module statistics report can be found here.
Markers Release Notes
This release of the Markers Module is mostly a maintainance build, fixing and updating the current set of data. As the module integrates information from the Genomes, QTL, and Genes Modules, see their release notes for any notable changes. Note that any updates to mappings are also reflected in the Maps Module. The database currently contains a total of 13,561,886 marker records from 253 species.
Marker breakdown by type
Marker Type Markers AFLP 8150 Breakpoint interval 303 Centromere 49 Clone 2561808 deletion 895 EST 4459675 EST Cluster 1325127 FPC 22651 Gene 9764 Gene Model 95297 Gene Primer 19 GSS 4750481 insertion 686 Maize Bin 100 mRNA 142037 other_dna 30601 OVERGO 16964 Primer 5398 QTL 11210 RAPD 174 RFLP 17739 SSR 14762 SSR Primer Pair 16883 STS 2234 Undefined 68879 Marker breakdown by species
Species Markers Barley (Hordeum spp.) 682030 Maize (Zea spp.) 4630429 Oat (Avena spp.) 8840 Rice (Oryza spp.) 5014771 Rye (Secale spp.) 13512 Sorghum (Sorghum spp.) 1293109 Sugarcane (Saccharum spp.) 340032 Wheat (Triticum spp. + Aegilops spp.) 1345414 Other 233749 A more detailed Marker Module statistics report can be found here.
Proteins Release Notes
The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.
- Total number of proteins: 97042
- Proteins from SWISS-PROT: 2628
- Proteins from TrEMBL: 94414
- Proteins with Pfam annotations: 57747
- Proteins with Prosite annotations: 32300
- Proteins with Signal peptide predicted by TargetP: 49857
- Proteins with Transmembrane domains predicted by TMHMM: 18516
- Proteins with Gene Ontology (GO): 65793
- Proteins with Plant Ontology (PO): 162
Ontologies Release Notes
Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.
For the first time QTLs are associated with the Plant Ontology terms. Click here for an example.
Ontology Total terms Total Terms w/Associations Total Associations Gene Ontology (GO) 23634 2474 347632 Plant Ontology (PO) 797 138 14180 Growth stage Ontology (GRO) 236 94 4699 Trait Ontology (TO) 779 460 13161 Taxonomy Ontology (GR_tax) 2526 1246 117906 Environment Ontology (EO) 497 49 552
Genes and Alleles Release Notes
Content: Number of genes
- Total -- 9227
- Rice -- 2544 (440 new genes include 284 siRNA genes)
- Maize -- 6680
- Sorghum 3--
Improvements include:
- Added 284 siRNA genes reported by Sunker et al., Nucleic acids research , 2005, 33, pp.4443-4454. If a siRNA was mapped to more than one chromosome the chromosome number is not provided.
- Many of the siRNA genes have "Target gene(s)" field added to their annotation. This section provides a list of rice gene models identified in the rice genome (available in Genome section) with which it is predicted to interact. e.g. GR:0100940, small interfering RNA P108-B7. The prediction is based on the in-silico analyses using the Vmatch sequence analysis software.
- Most of the rice genes with the first character of the gene symbol from "A" to "M" in our database now have ontology associations to TO, GO and PO.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database now contains a total of 11,209 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.
An improvement in this release is that all QTL have been described and annotated by multiple ontologies. In addition to Trait Ontology (TO) terms used in previous releases, Plant Ontology (PO) terms have been added to describe Plant Structure and Plant Growth and Development Stage associated with a particular QTL. Those terms have been annotated according to the information from QTL experiments in the cited literature, or by creating a default mapping based on the expertly identified TO and PO associations.
Another recent improvement is the addition of multiple QTL mapping positions when available. For rice QTL with genome positions, we currently provide the inferred positions on the Gramene Annotated Nipponbare Sequence map in addition to the original "experimental" QTL positions. These genome positions are displayed on both Gramene Maps and Genome Browser and will greatly enhance users' ability to do comparative mapping research.
A more detailed QTL database statistics report can be found here.
Pathways Release Notes (version 1.2)
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in plants: rice (Oryza sativa) and Arabidopsis thaliana and bacteria E. coli. This tool also allows you to draw comparisons among the data sets from the above three species.
Forty six pathways have been deleted during this round of curation. A list of the deleted pathways can be found here
A summary of the key components of RiceCyc is given below.
- Pathways: 279
- Enzymatic Reactions: 1687
- Transport Reactions: 5
- Polypeptides: 43172
- Protein Complexes: 4
- Enzymes: 10387
- Transporters: 62
- Compounds: 1265
This tool also allows you to upload your own gene expression data on the pathways to visualise an overview of the cellular level expression profile.
For more information please visit RiceCyc start page.
Diversity Release Notes
The Gramene Genetic Diversity database contains SSR allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
On this release:
- Rice: 695 germplasm accessions (651 unique); 572 SSR markers (254 unique).
- Wheat: 48 germplasm accessions; 3802 SNP markers.
- Maize: 449 germplasm accessions with SNP data; 1544 germplasm accessions with SSR data. 1435 SNP and 520 SSR markers.
Click here for database summary.
Version 23 - November 2006
Gramene Release 23 November 2006
This release includes:.
Gramene website features:
- Species pages A link to the species pages has been placed on the navigation bar at the top of page. These pages have been broken down into more but smaller pages, and the consistency of format between the species has been improved. Now you can navigate between species from any species page, not just from the introduction pages.
- Gramene Data Summary for select species: The species pages now have a summary overview of all the genomic data for that specie in Gramene. For an example see the Rice Data
Gramene Database:
- Genomes: Much new and updated data. Also, tree-based visualisation of orthologs/paralogs for rice/maize/arabidopsis. (See More info)
- Maps: (See More info)
- Markers: (See More info)
- Proteins: (See More info)
- Ontologies: We are making progress on integrating ontologies with other databases, as shown in their associations. (See More info)
- Genes: We're making progress in ontology associations to TO, PO or GO; new microRNA genes, and map position links. (See More info)
- QTL: New - when available you will find multiple links to QTL mapping positions and the inferred positions on the Gramene Annotated Nipponbare Sequence. (See More info)
- Pathways: (See More info)
- Diversity: (See More info)
Genomes Release Notes
New Genomes Data
- The browser tracks for EST/mRNA/GSS were updated with latest NCBI Genbank records
- New contigview tracks added to Rice genome browser
- MaizeCornchip0_ArrayConsensus_Affy8K: Maize Corchip0 array consensus sequences downloaded from Plexdb (mapping document)
- Sugarcane_ArrayConsensus_Affy8K: Sugarcane array consensus sequences downloaded from Affymetrix (mapping document)
- Imported 171 Oryza sativa miRNA genes from miRBase (for example: osa-MIR159b )
- Import of the Oryza rufipogon FPC map produced by the OMAP project (OP__B from Jan 2006). Check here.
- Mapping of the clones from the O. rufipogon FPC map to the rice genome based on the mappings of O.rufipogon BAC end sequences. Check here .
- Mapping of the FPContigs from the O. rufipogon FPC map to the rice genome based on the mappings of O.rufipogon clones. Check here .
- Tree-based visualisation of orthologs/paralogs between rice, Arabidopsis and maize gene models. (for example: Rice gene LOC_Os06g16370 ). The method used to generate the data is described in detail here .
Maps Release Notes
The Maps Module has been updated to the latest CMap 0.16 release. There have been numerous changes to both the code base and user interface, which should improve query response times as well as provide a more intuitive user interface.
With this release, all data (map sets, maps, features, and correspondences) in the Maps Module are built from the Markers Module. Users are encouraged to consult the Markers Module for primary information about markers and their mappings. The Maps Module should be considered to be primarily a visualization tool.
The Gramene Annotated Nipponbare Sequence no longer includes all features on the Ensembl Rice Genome Assembly, but only features that have correspondences to other maps. This was done to reduce visual clutter as well as improve server response time. All mappings are still present in the Markers Module and can be visualized in the Rice Genome Browser. The map set still includes all rice gene models. In addition, we have for the first added QTL to the map set.
To faciliate comparison with the OMAP physical maps, we have produced a new map set: OMAP Gramene Annotated Nipponbare Sequence. This map set includes features not exported to the regular Gramene Annotated Nipponbare Sequence map set. Furthermore, the OMAP FPC maps are also available as ordered maps. These ordered maps offer faster rendering and a more compact arrangement, where contigs are displayed as a single map rather than as individual entities. The order of contigs on these ordered maps is based on correspondences to a reference map, namely the rice TIGR genome assembly. The user may view contig and clone mappings based on BAC end sequence alignments across a given chromosome.
New and Updated Sequence Maps
- Rice-Gramene Annotated Nipponbare Sequence 2006
- Rice-OMAP Gramene Annotated Nipponbare Sequence 2006
New and Updated Physical Maps
- African rice-Non-anchored FPC OG_BB 2006
- African rice-Anchored FPC OG_BB 2006
- Oryza alta-Non-anchored FPC OA_BB 2006
- Oryza australiensis-Non-anchored FPC OA_AB 2006
- Oryza brachyantha-Non-anchored FPC OB__B 2006
- Oryza granulata-Non-anchored FPC OG_AB 2006
- Oryza minuta-Non-anchored FPC OM__B 2006
- Oryza nivara-Non-anchored FPC OR_BB 2006
- Oryza nivara-Anchored FPC OR_BB 2006
- Oryza officinalis-Non-anchored FPC OO__B 2006
- Oryza punctata-Non-anchored FPC OP__B 2006
- Oryza ridleyi-Non-anchored FPC OR_AB 2006
- Oryza rufipogon-Anchored FPC OR_CB 2006
- Oryza rufipogon-Non-anchored FPC OR_CB 2006
- Porteresia coarctata-Non-anchored FPC OC__B 2006
New Ordered Physical Maps
- African rice-Anchored Ordered FPC OG_BB
- Oryza alta-Non-anchored Ordered FPC OA_BB
- Oryza australiensis-Non-anchored Ordered FPC OA_AB
- Oryza brachyantha-Non-anchored Ordered FPC OB__B
- Oryza granulata-Non-anchored Ordered FPC OG_AB
- Oryza minuta-Non-anchored Ordered FPC OM__B
- Oryza nivara-Anchored Ordered FPC OR_BB
- Oryza officinalis-Non-anchored Ordered FPC OO__B
- Oryza punctata-Non-anchored Ordered FPC OP__B
- Oryza ridleyi-Non-anchored Ordered FPC OR_AB
- Oryza rufipogon-Anchored Ordered FPC OR_CB