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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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