1. Welcome to the Gene and Allele Database Tutorial
Gramene v. 26
Welcome to the Gene and Allele Database Tutorial
This tutorial will describe how to navigate the section of Gramene that provides descriptions of alleles associated with morphological, developmental, and agronomically important phenotypes and variants of physiological characters, biochemical functions and isozymes.
Many genes in Gramene also have map positions and sequencing data.
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2. Tutorial Tips
If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the left hand side of the Reader for easier navigation.
Note! Although we continually work to make Gramene compatible with all browsers, there are problems with some browser versions. If you're having difficulty viewing Gramene, try using a different browser. Please report any problems with browsers through Gramene Feedback.
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3. Click here to open gene search
Gramene Home Page
Click here to open gene search
See Navigation Tutorial for info on navigating Gramene
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4. Module Home-Page layout
Module home pages provide the following information:
Searching/Browsing – links to different types of searches.
Other Tools – if applicable, links to different tools used in this module.
Help – links to help pages, tutorials, release notes, FAQ and other helpful documentation.
Download – information on where to download the database.
Feedback – How to contact Gramene
Acknowledgements – Other programs that contribute to this data.
Quicklinks and external links – when appropriate these links are provided.
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5. Gene & Allele Database Home Page
Use * to search for wildcards
1. Use the “search” link from the gene menu to select a more limited (specific) search. (see slide 5) or
2. Use the general search option.
Description of Information in Gramene Gene and Allele Database:
For fully annotated genes, the database provides the following types of information to users:
General information:
Gene name: Traditional gene names have been used. Some gene names have been modified according to the Gene Nomenclature System.
Gene symbol: Gene symbols have been assigned, according to the Gene Nomenclature System.
Gene synonym: List of names or symbols that have been used for a specific gene.
Phenotypic description: Text defines the primary visual feature used to detect the phenotype for a particular gene to distinguish it from the wild type.
Phenotypic image: Display image(s) and text explanation of phenotypes for a particular gene, if available.
Gene accession and gene product:
GenBank accession: Provides the link to NCBI, if the related GenBank accession number is available.
Gene product: Provides the link to the Gramene Protein Database, if available.
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.
Allele designation: 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 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.
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.
Year: The year when the study was done. If not available in "Materials and Methods", the year of the publication will be used.
Season: The seasons in which the study was done.
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.
Study type: Choices include field, greenhouse, growth chamber, and laboratory.
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.
Map position: Shows closely linked markers, map name, chromosome number, start position and stop position on a particular map.
Associated feature: One or multiple composite associated terms are used to define the associated feature for the particular gene. The composite associated term consists of:
Trait ontology term (TO)
Developmental stage (PO)
Anatomy location term (PO)
Biological process term (GO)
Evidence code
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. It also gives an option to search in Gramene Literature database for all the references that may be associated with this entry.
For the genes under curation, the database currently provides the following core information to the user:
Gene symbol: Gene symbols have been assigned following the Gene Nomenclature System.
Oryzabase link: Provides the link to the curation page for the same gene in Oryzabase , if available.
Explains module navigation menu,
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6. Search Options Option 1. Click an ontology to search ontologies db.
Option 2. Search by term
Click search icon
Optionally, select field name, gene type, species, and whether or not the gene is associated with a known phenotype.
Option 1: Search by term (next slide)
Option-2: Browse for a gene via Ontology Database
The user can browse genes by searching for a trait in the Ontology Database.
Go to the Trait Ontology Database in Gramene.
Type the particular trait or Gramene trait accession ID in the search field (e.g. cold tolerance or TO: ), select "Trait (TO)" and click "Search" button. The summary page for the particular TO term will display.
In above page, a list of the gene(s) related with the particular TO term will be displayed in the "Phenotype Association" field.
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.
Go to the Plant Structure Ontology Database in Gramene.
Type the particular plant structure keyword or Gramene plant structure accession ID in the search field (e.g. seed or PO: ), select "Plant structure (PO)" and click "Search" button. The summary page for the particular PO term will display.
In above page, a list of the gene(s) related with the particular PO term will be displayed in the "Phenotype Association" field.
The user can browse genes by searching for a plant growth stage keyword in the Ontology Database.
Go to the Plant Growth Stage Ontology Database in Gramene.
Type the particular plant growth stage keyword or Gramene plant growth stage accession ID in the search field (e.g. tillering or GRO: ), select "Growth stage (GRO)" and click "Search" button. The summary page for the particular GRO term will display.
In above page, a list of the gene(s) related with the particular GRO term will be displayed in the "Phenotype Association" field.
Option-3: Browse for a gene via Literature Database The user can browse genes by searching literature citations in the Literature Database.
Go to the Literature Database in Gramene.
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.
Selecting a specific citation from the above summary page, and clicking "More info" will guide the user to the particular page for that citation.
In the above page, a list of the gene(s) related with the particular citation (if any) will display in the "Associated Data" field.
Click on the "gene" link for detail on this (these) gene(s). (e.g. GR: )
Be aware of wildcards. For example, searches for *dwarf, dwarf*, and *dwarf* will all give different results.
Option 3. You may also browse for a gene via Literature Database. Go to the Literature Database in Gramene. Literature detail will display genes in the “Associated Data" field.
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7. Results for Gene Search by Term / Key word
There are 99 entries for rice genes with CDS and phenotype
Click to view next 25 results as needed.
Click on linked column headings to sort table by that column
Click on a gene symbol to view the detail page for that particular gene (for tutorial select “d1” and see slide 9)
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8. Gene Detail Page General Info
Gene detail is displayed along the top. See Help file for term definitions.
Associated Data is under the Gene detail. The number represent numbers of associations. Click a category to expand the table and access that data in Gramene (see slides 8–13). Grayed-out categories have no associations.
# For fully annotated genes, the database provides the following types of information to users:
# General information:
* Accession: Gramene internal unique accession.
* Gene name: Traditional gene names have been used. Some gene names have been modified according to the Gene Nomenclature System.
* Gene symbol: Gene symbols have been assigned, 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.
Gene detail may vary by species, depending upon level of curation.
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9. Gene Associations – Allele and Germplasm Info
Links to Ontology DB
Allele:
Allele designation: 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 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 authaer, 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.
Allele and Germplasm categories show one or multiple items for a particular gene. Click a name to view its summary
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10. Gene Associations - Sequences
Click on protein to view more information from Gramene’s Protein database (See Protein tutorial). Link to GenBank for sequence info
Click GenBank ID to view the nucleotide sequence link for each protein from the National Center for Biotechnology Information.
Select Ensemble Gene to view Tigr gene report in Genomes database (See Genomes tutorial).
Click on IRGSP gene name to go to the Rice Annotation Project DB (RAP-DB)
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11. Gene interactions
If it is known that a gene interacts with another gene, that will be noted here.
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12. Genes – Map Positions Preview comparative map
# Map position: Shows closely linked markers, map name, chromosome number, start position and stop position on a particular map.
Select to view the highlighted gene in Maps or on the genome browser (See Maps and Genomes tutorials).
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13. Genes – associated ontologies
# Associated feature: One or multiple composite associated terms are used to define the associated feature for the particular gene. The composite associated term consists of:
* Trait ontology term (TO)
* Plant growth stage (GRO)
* Plant structure term (PO)
* Gene ontology term (GO)
* Environment ontology term (EO)
Click links to go to the Ontology Database within Gramene. (See Ontology tutorial).
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14. Gene - Associated References
Click to view Oryzabase’s information on the selected gene.
# 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. It also gives an option to search in Gramene Literature database for all the references that may be associated with this entry.
Click reference info to go to the reference in Gramene Literature database (See Literature tutorial).
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15. Gene - Images
When there are images in the database associated with a phenotype gene, they will display here.
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16. How to Submit Newly Identified Genes
Click here to submit a gene to the database.
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 using the PDF file: The user can also use this PDF form to 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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17. Help Documents
Help documentation gives detailed notes about the information found in the database, and help on using the search tools.
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18. Tutorial
Tutorial shows the features of a database. Tutorials come in PowerPoint and PDF. Some are also available in MS Word.
Navigate to other Gramene tutorials.
Links to download software for viewing tutorials.
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19. FAQ’s Feedback: Submit a question to Gramene Search FAQ
Click questions to expand or collapse a question or answer
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20. Email Gramene List-serve at gramene@gramene.org
Contact Gramene
Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or
Gramene List-serve at
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