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intron sequences

Mike Cherry cherry at GENOME.STANFORD.EDU
Fri Jul 12 22:58:27 EST 1996


Bert Liang (liangb at essex.uchsc.edu) wrote:
> I have been searching for the yeast intron sequences aI1 and aI2 in 
> the gene COX1 (from yeast mitochondria) from S. cerevisiae; I have 
> looked in the Stanford and Biosci archives, as well as the yeast GDB 
> without success.  Could someone point me in the right direction?
> 
> Thanks for any help.
> 
> Bert Liang
> liangb at essex.uchsc.edu
> 

The aI1 and aI2 can be found in SGD in the Locus class.  Go to the
home page click on "Search".  A locus search is the default search,
that is what you need.  Type in aI1 and click "Submit".  You will now
see the info on the gene aI1.  A CDS from a GenBank entry is available
for aI1.  You can click on "Retrieve DNA" to get just the DNA of the
ORF, or you can click on "L36897_1.cds" to see the info on the CDS
from GenBank.  Protein sequence and YPD links are also available if
thats what you want.  You can see the GenBank or EMBL entry from the
L36897_1.cds page, clicking on the "YSCMTCG13 (GB)" link, and then
clicking on either GenBank or EMBL.

There is no sequence associated with the aI2 Locus entry in SGD.  This
is because there is no GenBank entry that states where aI2 is located.

You can get all the introns of COX1 by searching for COX1 and then
looking at one of the CDS sequences.  For example with V00694_1.cds
you will see a list the eight exons.  You can need retrieve the DNA of
the region you want.  Note that not all the CDS entries for COX1 are
full length, and not all the GenBank entries that cover COX1 have the
gene annotated.

Mike

    Address for the Saccharomyces Genome Database Project (SGD)
             e-mail:    yeast-curator at genome.stanford.edu
          Telephone:    415-725-8956

    General Addresses for Genome Databases at Stanford
                ftp:    genome-ftp.stanford.edu
             Gopher:    genome-gopher.stanford.edu
                WWW:    http://genome-www.stanford.edu/
                FAX:    415-723-7016



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