BFG@University of Richmond

Wednesday, October 12, 2005

Finding mutations in FlyBase


An important way to test the in vivo function of a protein is to compare the phenotype of normal (wild type) individuals to the phenotype of individuals lacking the function of a particular gene. By studying the defects associated with loss of gene function, we can make inferences about normal gene function. Drosophila melanogaster is a great model organism for doing these types of experiments, as there is a treasure trove of genetic resources available. How can you find mutations in a particular gene? There are a number of ways:

1) FlyBase gene query.

Go to FlyBase home page.
Click on the Genes link.
Click on Genes Search link.
Type in gene name (CGnnnn or actual gene name) and click submit button. For example, I did this with the Kinesin light chain (Klc) gene. The results page has lots of results; be sure to pick the correct one!
The Synopsis of the Klc FlyBase entry has lots of information about the size of the protein and its function. We are interested, however, in finding mutations in the Klc gene.
The first place to look is at the Stocks link on the right side of the page. Not all genes have mutant stocks available at the Stock Center, and some mutations that are available have not been ascribed to your favvorite gene (even though they do exist). How can you find such mutations?
Click on the Gene Region Map link on the right side of the page. A map representing the part of the genome in which your favorite gene resides will appear. The map is clickable, and map data can be changed using the toggle buttons at the bottom of the page. Useful buttons include transgene insertion site, deleted segments, and transgene insertions. Click the buttons you wish to try (one at a time at first), and then click the update map button. Click on new features that appear on the map for more information.
What if this approach yields no results? One approach is to search the Special Collections of fly mutations, especially the Baylor/BDGP Gene Disruption Project and the Exelixis Collection.

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