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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.

Welcome to the Gene and Allele Database Tutorial

Gramene v. 26

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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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Gramene Home Page

Click here to open gene search

See Navigation Tutorial for info on navigating Gramene

www.gramene.org

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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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Gene & Allele Database Home Page

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.

Use * to search for wildcards

Explains module navigation menu,

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Option 1. Click an ontology to search ontologies db.

Search Options

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.

Click search icon

Optionally, select field name, gene type, species, and whether or not the gene is associated with a known phenotype.Be aware of wildcards.

For example, searches for *dwarf, dwarf*, and *dwarf* will all give different results.

Option 2. Search by term

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Results for Gene Search by Term / Key word

Click to view next 25 results as needed.

There are 99 entries for rice genes with CDS and phenotype

Click on linked column headings to

sort table by that columnClick 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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Gene detail is displayed along the top. See Help file for term definitions.

Gene Detail Page General Info

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.

Gene detail may vary by species, depending upon level of curation.

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Allele and Germplasm categories show one or multiple items for a particular gene. Click a name to view its summary

Gene Associations – Allele and Germplasm Info

Links to Ontology DB

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Gene Associations - SequencesClick 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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Gene interactions

If it is known that a gene interacts with another gene,

that will be noted here.

04/22/23 12Select to view the highlighted gene in Maps or on the genome browser (See Maps and Genomes tutorials).

Genes – Map Positions

Preview comparative map

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Click links to go to the Ontology Database within Gramene. (See Ontology tutorial).

Genes – associated ontologies

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Click reference info to go to the reference in Gramene Literature database (See Literature tutorial).

Click to view Oryzabase’s information on the selected gene.

Gene - Associated References

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Gene - Images

When there are images in the database associated with a phenotype gene, they

will display here.

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How to Submit Newly Identified Genes

Click here to submit a gene to the database.

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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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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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FAQ’s

Search FAQ

Feedback: Submit a question to Gramene

Click questions to expand or collapse a question or answer

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Contact Gramene

Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene.

Email Gramene List-serve at gramene@gramene.org

or