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Gramene Genes & Alleles Database Help Document

Genes & Alleles search/browse options

A. Quick Search

From the Genes home page, enter a keyword into the "Quick Search" Box, and click on the search icon. Use "*" as a wildcard. For example, searching "*dwarf-1*" will give results for dwarf and semidwarf, with numbers begining with "1", such as "1" or "19"

B. Simple Search

1. Browse by Ontology

   1. In the "Associations" section for your term of interest a list of the gene(s) (if any) related with the particular TO term will be displayed, along with the number of genes. Click on the species of interest.
   2. The next page will list all the genes for the ontology term. Click on the "Object Acession ID" which links to the Gene page for that gene. (e.g. Cold tolerance at seedling stage-2)

2. Text Search

   1. Enter a keyword in the search box. Use "*" for a wildcard, as described above for "Quick Search".
   2. Select the field to search for this term. Options include:

      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

   3. Optionally - select the gene type to filter your results. Gene types include:
      • Not sequenced
      • CDS (Protein coding)
      • rRNA (Ribosomal RNA)
      • tRNA (Transfer RNA)
      • Pseudogene (non-functional)
      • Not classified
   4. Optionally, narrow your search to a single species by selecting the species of interest.
   5. If you want the results to only show genes for which phenotype information is available, select the "Has Phenotype" option.

3. Browse Literature Database

   1. Go to the Literature Database in Gramene.
   2. Type author, key word, or journal name in the search field and click "Search" icon. (e.g. dwarf)
   3. Select a specific citation from the above summary page and click "View Reference."
   4. A list of the gene(s) related with the particular citation (if any) will display in the "Associated Data" field (example).
   5. Click on the species of interest and follow the links to the gene information.)

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Genes Search Results

The database provides the some or all of the following types of information, depending on the level of curation:

• General information:
• Species: Species which the gene belongs to.
• 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.
• Synonyms: List of names or symbols that have been used for a specific gene.
• E.C.Number(s): Provides E.C.Numbers related with the gene if feasible.
• 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.
• 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.
• Synonyms
• 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.
7. Alleles
8. References
• Germplasm
• Genes
• Associated Ontologies
• 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.
• 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.
• Alleles
• Genes
• Sequences:
• 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.
• Gene-to Gene-Interactions
• Gene Interactions
• Map position: Shows closely linked markers, map name, chromosome number, start position and stop position on a particular map.
• Gene Map Position
• Associated Ontologies: 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)
• Plant Growth and Development Stage (PO, Plant ontology)
• Cereal Growth Stage (GRO, Growth stage ontology)
• Cellular Component (GO, Gene Cellular Component Ontology)
• Molecular Function (GO, Gene Ontology-Molecular function)
• Biological process (GO, Gene Ontology-Biological process)
• Environment (EO, Environment ontology)
• Associated QTL
• Database Cross-References:
• Oryzabase link if available, and a list of references in Gramene that are related to the gene.
• Images: (if available) Display image(s) and text explanation of phenotypes for a particular gene.

Other Resources

Tutorial	More in-depth than the help pages, use the tutorial for an exaple of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ	Frequently Asked Questions - see what questions users have asked, and get the developers answers.
Release Notes	For more information about the most recent release.

Feedback

• Please suggest additional fields you'd like to search for by either using the "Feedback" link at the top of the Gramene pages or by going to the following URL: /db/feedback/send_feedback?refer_from=/rice_mutant/index.html
• If you find any inconsistencies or mistakes, please communicate them to us by clicking on the "feedback" link. Your suggestions and feedback are highly appreciated by the Gramene staff.
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How to submit a gene at Gramene:

Option 1: Submit on line:

A web-based submission form to submit newly identified genes that are accepted for publication or already available in scientific publications.

Option 2: Submit by regular mail:

Print out form from abome, and mail completed form to:
Gramene Curation Group
G-15 Bradfield Hall, Plant Breeding
Ithaca, NY 14853, USA

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