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1. Identifying the list of annotated genes between two markers.
For this example we will use an obesity QTL:
Obq7: flanked by (D1Mit213, D1Mit131) peak(D1Mit76)

By Text Search
From the Map Viewer home page (http://www.ncbi.nlm.nih.gov/mapview/) you can go to the home page for the organism in which you are interested by opening the menu under the proper clade and selecting the organism name. You can also search from the Map Viewer front page by selecting the organism of interest from the pull-down menu on the top of the page. An advanced search page is available from the organism specific page.

The appropriate syntax for the search is to join the two flanking markers with the boolean OR.
ex. D1Mit213 OR D1Mit131

Performing the simple search will return a graphical and tabular view showing every map and location containing an object with either of these names. You can use the advanced search to limit the search to a particular object type (STS, Gene, etc) or to particular maps (sequence based, non-sequenced based, etc).

From the results page, clicking on the blue chromosome number will give you all of the matches found on the reference assembly for that chromosome. Clicking on the 'all matches' link in the tabular view will give you all of the matches on a given assembly for that chromosome. Clicking on the marker in the tabuler view will bring up the maps on which this particular map is found (plus a couple of additional default maps). Clicking on a particular map will bring up only that map.

Two see both markers, click on the chromosome. One of the default maps shown is the Genes Map. The Maps&Options button will produce a pop-up menu that will allow you to add and remove maps, as well as adjust map order.

Once the appropriate view has been obtained genome coordinates can be obtained by using the 'Data as Table' button (although the number of results that can be obtained is limited).

By Sequence Search
If you are not using publicly available STSs for mapping, the STSs can be localized on the genome using Reverse e-PCR (http://www.ncbi.nlm.nih.gov/sutils/e-pcr/).
For this example, we will go to UniSTS to obtain the primer sequences and anticipated product size, and then run reverse e-PCR. The results from this analyis are linked to the Map Viewer.