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Questions and Answers (continued)

10) How to find the names of BACs corresponding to your favorite [mouse?] gene?

Let us assume, for example, that we want to find BACs containing the complete mouse CDK2 locus. How and where to we find this information?

There are different routes to find clone ID's and we will explain one of these, which makes use of the University of California at Santa Cruz (UCSC) Genome Browser. Other routes might include the recently expanded (late 2008) NCBI CloneFinder program. The UCSC and NCBI links will open the Mouse Genome Browser and the Mouse Clone Finder program. If you're interested in a different species, change the species name for the Browser/CloneFinder and then proceed.

The following text applies only to the UCSC Browser. Type the gene name in the "position or search term" window to replace the default text. In this case, type CDK2.  Click the "Submit" button. A new page with many search results with data relevant to "CDK2" appears. Make your best selection based on your own knowledge of the gene and click the related link to open the Genome Browser. For instance click on a link with the specific label "(NM_183417) cyclin-dependent kinase 2 isoform 1 " (you can find this below the heading "RefSeq Genes"  Once you click on this link, you will get a map encompassing the genomic features of a 7,068 bp chromosome segment. You can change the display: zoom in or zoom out, display additional genomic features, etc. You may also see a series of horizonal lines under he heading of "BAC End Pairs" and horizontal lines have arrow heads pinting to the left or the right. This polarity indicates the relative orientation of the insert and vector sequences. If you don't see any horizontal lines and a "BAC End Pairs" heading, then you will need to activate the "BAC End Pair" display option on the Genome Browser to "Full".  If you see the BACs, how do you know the size and boundaries of the BAC insert sequence? You can either zoom out until you see the two insert ends displayed, or you can click on one of the horizontal "BAC" lines. When you click, a new page opens with many links to the related BAC-insert End Sequences ("BES").

Anyhow, you will likely have found many BACs containing the small CDK2 locus and most of the displayed BACs have a name starting with "RP", either "RP23" or "RP24". Occasionally, BACs with a "MSMG01" pre-fix will be seen. These prefixes iindicate the names of the specific BAC libraries which include these BAC clones. The "RP23" and "RP24" BAC libraries were made in our BACPAC laboratory and a more extensive description can be found on the corresponding pages in our BACPAC library browser. You will discover that both of these libraries are derived from the C57BL/6J strain. We have many additional murine BAC libraries from different strains, but BAC clones corresponding to specific genes for these additional libraries cannot be found in databases. The libraries have to be screened. See for instance, our "Screening Service". The BACs with the MSMG01 prefix are derived from a wild Asian mouse subspecies ("Mus musculus molossinus") and this BAC library is not part of our BACPAC Resource Center but available through the RIKEN Institute in Japan. The complete BAC names follow the NCBI recommended clone nomenclature rules.


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