Problem:
You have a region of the rat genome identified (chr12: 9194687 - 39194687) and you want to know what microsatellite markers lie within that region.
Solution:
The first step is to select the RGD Microsatellite Markers database from the martveiw page.
(Click Here to open Martview in a new window.)
We then click on "Filters" from the side bar. This will bring us to our filters page. We check the first box, select chromosome 12 and enter in the start
and stop position in base pair value for our region.
We now click on "Attributes" from the side bar to go to the attributes page. We select RGD ID, Symbol, and Start and Stop. We then click the Results button. This will return a preview
of all the markers that are wholey or partially fall in our region.
Discussion
The SSLP Biomart can also be used to export the size of a microsatellite marker for a given rat strain. This can be used to indentify polymorphic
markers between two or more inbred strains so that these markers can be used in genetic mapping studies. If you are interested in the selection
of polymorphic markers or a more graphical view of the allele data in different starins please have a look at the RGD Genome Scanner and ACP Haplotyper tools.
These use the same microsatellite allele data and provide a custom web interface specifically designed to address these common research problems.
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