Gramene Oryza Queries

Show me all the markers that start with "RM."

To perform this query, open the Markers database by using the main navigation bar of Gramene.
Use the Marker navigation bar to open the Marker Search function.
Type RM* in the "Search for markers" box and select "Submit Query".
A "Marker search results" page will appear with a list of all available microsatellite markers in Gramene.
Note: "RM*" can be replaced to perform similar marker searches.

Show me all the QTL associated with "biotic stress."

To perform this query, open the QTL database by using the main navigation bar of Gramene.
Use the QTL navigation bar to open the QTL Simple Search function.
Using the "Search by Trait Category" option, click on "Biotic stress."
A QTL search results page will appear with a list of all traits associated with biotic stress.
Note: "Biotic stress" can be replaced by any other QTL trait category to perform similar searches.

Show me all available information associated with the "dwarf" gene.

To perform this query, open the Genes database by using the main navigation bar of Gramene.
Use the Gene navigation bar to open the Search function.
Type "dwarf*" in the "Gene Search" box, select "all fields" and select "Search".
A "Summary" page will appear with a list of genes associated with dwarf stature in Gramene.
Selecting one of the genes will provide a detailed Summary page.
Note: Use the wildcard * in a search when you don't know the exact term you are searching.

What are the best maps to use to compare rice to maize?

To perform this query, open Maps-CMap (Gramene's comparative map viewer) by using the main navigation bar of Gramene.
Use the CMap navigation bar to open the Matrix.
In the "Restrict Reference Sets By" section, select rice from the "All Species" field, and then click on "Submit."
A Matrix results table will appear. Down the page vertically, all the rice maps will appear. Across the page horizontally, all the other maps will appear.
Scroll horizontally until you reach the maize section. The numbers in the individual cells indicate the number of correspondences the maps contain, i.e., the greater the number, the better the rice map to compare to maize.
Note: Rice can be replaced with any other species in Gramene to perform similar searches.

How can I find information on a QTL from an article I read recently on rice quality, and estimate its position on the rice genome?

To begin, open the database by using the main navigation bar of Gramene.
Enter any of the search terms from the article into the Search function. For this example, type in the article key words "rice quality".
A Literature search results page will appear, and you can look for the article pertaining to your interests. Click on the article's (More Info) selection.
The "Associated Data" field provides information on any QTL, genes, proteins or markers that Gramene carries information on. Selecting the QTL association will provide a list of all associated QTL.
Click on a QTL accession to produce a "QTL detail" page.
Selecting "View On Map" from the "Map Position" field from that page
Notice marker RM589. It is the nearest flanking marker to the QTL. Clicking on the marker will produce a "Feature detail" page that provides the start and stop position of the marker. You may also view that marker on the Genome Browser.

How do I obtain the peptide sequence of a rice protein?

For this example, the gene Pi-ta will be used.
To perform this query, open the Protein database by using the main navigation bar of Gramene.
Type Pi-ta in the "Search" box and select "Search".
A table of matching records will be displayed. Selecting an "Accession No." will provide a "General Information" page.
Click on the last item in the protein menu: "FASTA sequence".

How many copies of my gene of interest are there in the rice genome and where are they located?

Obtain your sequence. You may use a protein or DNA sequence. If a particular protein is not located in Gramene, GenBank can be used. Pi-ta's GenBank accession is AF207842. Display its FASTA format and copy the sequence.
Open BLAST by using the main navigation bar of Gramene.
Paste the sequence into the "Enter the Query Sequence" field.
This will produce a BLAST results page. Examine the images of the chromosomes. Depending on the user's tolerance for percent similarity, the user can infer how many copies there are (darker reds are closer matches).
To find the location of the copy, hover your mouse over one of the side arrows on the chromosome images that indicates a hit.A pop up menu will appear and selecting "ContigView" to view it on the genome. The location of the gene is provided in the "Detailed View."
Note - if you were in the Gramene protein database, you can select the link "Click here to generate a BLASTP query" as a shortcut.

What are the predicted exon / intron boundaries for a gene of interest?

Locate your gene on the genome browser. The gene's model prediction can also be found in the Detailed View of the Genomes, in the GeneModel_TIGR section. (Note - go to the detailed view, not the overview!)
Clicking on a TIGR gene will produce a pop up menu. (For this example, the popup on click and show popup menus have been selected from the decorations options in the detailed view. You may get different results if you have different selections. If you deselect the popup on click, hovering over a feature will reveal the popup menu. If neither option is selected, clicking on a feature will take you to an appropriate page with more information on that particular feature.)
Selecting "Gene" will produce a "Tigr_gene Gene Report" page, with the predicted model.

Are there any ESTs or full length mRNAs for a particular gene in rice and if so, how many and where are they from?

Locate your gene on the genome browser. ESTs, CDS and cDNAs will appear as displayed features in the Detailed View of the Genomes. To make sure ESTs and other features will appear in your Detailed View (if available), check to see if they are selected to appear. This can be done by selecting "Features" and "ESTs" or any of the other drop down menus in the Detailed View. In the drop down menu that appears, select those ESTs or other features from either a particular species or all available species that you would like to be displayed (closing the window will refresh your view).

Are there any Tos 17 mutations in a gene of interest?

Locate your gene on the genome browser. If there are any Tos 17 mutations, they will appear in the Detailed View.
Note - Check to see that Tos 17 mutations are selected to be displayed in the Markers drop down menu.