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How to Search/Browse/Access the Gramene Genes Database

Option-1: Search for a gene

The user can search the Gramene Genes Database by typing a keyword and selecting the species field and any one of the following selection fields:

• Gene Symbol & Name
• Gene Accession
• Chromosome No.
• TO:Trait
• PO:Plant Structure
• GRO:Growth Stage
• GO:Cellular Component
• GO:Molecular Function
• GO:Biological Process
• EO:Environment
• GenBank Accession
• Gramene Protein Accession

For example, in order to find the gene dwarf-15, the user can type gene symbol, dwf15 or gene name, dwarf-15 in "Search for" field, select "Gene Symbol & Name" in "Search in", and select "Rice" in "Species", and then submit his search to find the related information. Also, the user can include wild cards in "Search for" field, so, with a searching of "*tillering stage*" for "GRO:Growth Stage", the user can find all genes associated with the tillering stage.

The user can also select "has phenotype" or use the following gene types to filter his research results:

• Not sequenced
• CDS (Protein coding)
• rRNA (Ribosomal RNA)
• tRNA (Transfer RNA)
• Pseudogene (non-functional)
• Not classified

For instance, the user can select "CDS (Protein coding)" in the "Gene Type" field and further choose "has phenotype" to find all genes with both coding sequence and phenotype information available.

Option-2: Browse for a gene via Ontology Database

The user can browse genes by searching for a trait in the Ontology Database.

1. Go to the Trait Ontology Database in Gramene.
2. Type the particular trait or Gramene trait accession ID in the search field (e.g. cold tolerance or TO:0000303), select "Trait (TO)" and click "Search" button. The summary page for the particular TO term will display.
3. In above page, a list of the gene(s) related with the particular TO term will be displayed in the "Phenotype Association" field.
4. Clicking "Associated Gene Name" will guide the user to the related gene page. (e.g. Cold tolerance at seedling stage-2)

The user can browse genes by searching for a plant structure keyword in the Ontology Database.

1. Go to the Plant Structure Ontology Database in Gramene.
2. Type the particular plant structure keyword or Gramene plant structure accession ID in the search field (e.g. seed or PO:0009010), select "Plant structure (PO)" and click "Search" button. The summary page for the particular PO term will display.
3. In above page, a list of the gene(s) related with the particular PO term will be displayed in the "Phenotype Association" field.
4. Clicking "Associated Gene Name" will guide the user to the related gene page. (e.g. Cold tolerance at seedling stage-2)

The user can browse genes by searching for a plant growth stage keyword in the Ontology Database.

1. Go to the Plant Growth Stage Ontology Database in Gramene.
2. Type the particular plant growth stage keyword or Gramene plant growth stage accession ID in the search field (e.g. tillering or GRO:0007049), select "Growth stage (GRO)" and click "Search" button. The summary page for the particular GRO term will display.
3. In above page, a list of the gene(s) related with the particular GRO term will be displayed in the "Phenotype Association" field.
4. Clicking "Associated Gene Name" will guide the user to the related gene page. (e.g. Cold tolerance at seedling stage-2)

Option-3: Browse for a gene via Literature Database

The user can browse genes by searching literature citations in the Literature Database.

1. Go to the Literature Database in Gramene.
2. Type author, key word, or journal name in the search field (e.g. Wessler SR , rice genome , Rice Genetics Newsletter), and click "Search" button The summary page for the particular author, key word, and journal will display.
3. Selecting a specific citation from the above summary page, and clicking "More info" will guide the user to the particular page for that citation.
4. In the above page, a list of the gene(s) related with the particular citation (if any) will display in the "Associated Data" field.
5. Click on the "gene" link for detail on this (these) gene(s). (e.g. GR:0060671)

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Description of Information in Gramene Genes Database:

For fully annotated rice genes, the database provides the following types of information to users:

• General information:
• Accession: Gramene internal unique accession.
• Gene symbol: Gene symbols have been assigned, according to the Gene Nomenclature System.
• Gene name: Traditional gene names have been used. Some gene names have been modified according to the Gene Nomenclature System.
• Gene synonym: List of names or symbols that have been used for a specific gene.
• Species: Species which the gene belongs to.
• Chromosome No: Chromosome or linkage group on which the gene is located.
• Gene Type: A particular gene has been categorized into the following gene types: "Not sequenced", CDS (Protein coding), rRNA (Ribosomal RNA), tRNA (Transfer RNA), Pseudogene (non-functional), and "Not classified".
• Has Phenotype: Show whether a gene has phenotype or not.
• Description: Text defines the primary features used to detect the phenotype and other related information for a particular gene to distinguish it from the wild type.
• Phenotypic image: (if available) Display image(s) and text explanation of phenotypes for a particular gene.
• Curator comment: Curator's comments on the nucleotide and protein sequences related with the gene if they are feasible.


• Allele: Shows one or multiple allele names for a particular gene. Detailed information for the specific allele can be displayed when you click the allele name.
• Accession (Allele accession): Gramene internal unique accession for the allele.
• Allele symbol: Different alleles of the same gene are distinguished by a decimal between the name of the gene and the number that follows, e.g., gle1.1. The synonyms for that allele are also listed following the allele designation.
• Allele name: Allele name if feasible.
• Allele description: Provided if alleles give phenotypic differences.
• Description of allelic interaction: Provided if the information about the interaction with other alleles or loci is available.
• Study: Provides a list of one or several studies or assays for that particular allele. Detailed information for a specific study can be displayed when you click the study's name.
1. Study name: Constructed of [name of first auther, principal investigator, or institution] + [year of publication or data submission] + [a, b, c . . .] to differentiate among multiple studies for the same investigator and year.
2. Year: The year when the study was done. If not available in "Materials and Methods", the year of the publication will be used.
3. Season: The seasons in which the study was done.
4. Location: The nearest city, town or university and institute name where the study was done. If not available in "Materials and methods," first author or principal investigator's address will be used to derive the location.
5. Study type: Choices include field, greenhouse, growth chamber, and laboratory.
6. Environmental factors: Text description of environmental conditions for a particular study, including temperature, light quality and intensity, moisture and nutrients, etc.


• Germplasm: Shows one or multiple germplasm names for the particular gene. Detailed information for a specific germplasm can be displayed when you click the germplasm name.
• Germplasm Accession: The germplasm accession or cultivar name which is associated with the gene.
• Location The laboratory where the related germplasm was used to do the genetic study for the gene.
• Wild Type: The germplasm accession or cultivar name of the wild type which was used to generate the mutant line.
• Mutagen: Mutagen used to generate the mutant allele.
• Mutagenesis Method: Detailed mutagenesis method used to generate the mutant allele.


• Sequence association:
• Protein: Provides the link to the Gramene Protein Database, if available.
• Nucleotide (DNA): Provides the link to NCBI, if the related GenBank accession number is available.


• Map position: Shows closely linked markers, map name, chromosome number, start position and stop position on a particular map.



• Ontology association: One or multiple composite associated terms are used to define the associated feature for the particular gene. The composite associated term consists of:
• Trait(TO (Trait ontology))
• Plant structure(PO (Plant structure ontology))
• Growth stage (GRO (Growth stage ontology))
• Molecular function (GO (Gene Ontology-Molecular function))
• Biological process (GO (Gene Ontology-Biological process))
• Environment (EO (Environment ontology))


• Reference:
• Oryzabase link:Provides the link to the curation page for the same gene in Oryzabase, if available.
• E.C.Number(s): Provides E.C.Numbers related with the gene if feasible.
• References used for curation: A list of all references related to the gene.

For the rice genes under curation, the database currently provides the following core information to the user:

• General information:
• Accession: Gramene internal unique accession.
• Gene symbol: Gene symbols have been assigned, according to the Gene Nomenclature System.
• Gene name: Traditional gene names have been used. Some gene names have been modified according to the Gene Nomenclature System.
• Gene synonym: List of names or symbols that have been used for a specific gene.
• Species: Species which the gene belongs to.
• Chromosome No: Chromosome or linkage group on which the gene is located.
• Gene Type: A particular gene has been categorized into the following gene types: "Not sequenced", CDS (Protein coding), rRNA (Ribosomal RNA), tRNA (Transfer RNA), Pseudogene (non-functional), and "Not classified".
• Has Phenotype: Show whether a gene has phenotype or not.
• Phenotypic image: (if available) Display image(s) and text explanation of phenotypes for a particular gene.


• Map position: Shows closely linked markers, map name, chromosome number, start position and stop position on a particular map.



• Reference:
• Oryzabase link:Provides the link to the curation page for the same gene in Oryzabase, if available.
• References used for curation: A list of all references related to the gene.

For the maize genes integrated from MaizeGDB, the database currently provides the following core information to the user:

• General information:
• Accession: Gramene internal unique accession.
• Gene symbol: Gene symbol based on the MaizeGDB for a particular gene.
• Gene name: Traditional gene name.
• Gene synonym: List of names or symbols that have been used for a specific gene.
• Species: Species which the gene belongs to.
• Chromosome No: Chromosome or linkage group on which the gene is located.
• Gene Type: A particular gene has been categorized into the following gene types: "Not sequenced", CDS (Protein coding), rRNA (Ribosomal RNA), tRNA (Transfer RNA), Pseudogene (non-functional), and "Not classified".
• Has Phenotype: Show whether a gene has phenotype or not.
• Description: Text defines the primary features used to detect the phenotype and other related information for a particular gene to distinguish it from the wild type.


• Map position: Shows closely linked markers, map name, chromosome number, start position and stop position on a particular map.



• Reference:
• MaizeGDB link:Provides the link to the curation page for the same gene in MaizeGDB, if available.

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How to submit a gene at Gramene:

Option 1: Submit on line:
A web-based submission form allows the user to submit newly identified genes that are accepted for publication or already available in scientific publications.

Option 2: Submit by regular mail:
The user can also use the previous submission form, print a hard copy, complete it, and mail it to:

Gramene Curation Group
G-15 Bradfield Hall, Plant Breeding
Ithaca, NY 14853, USA

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