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restriction fragments of 18S rRNA

Mike Cherry cherry at genome.stanford.edu
Mon Apr 5 17:02:05 EST 1999


> 
> I am trying to determine the sizes of the BAMH1, HIND111 and ECOR1
> fragments from 18S rRNA gene. How and where would I find this
> information.
> 
> Thank you for your help
> 
> 

SGD provides software on the Web to provide you this type of
information.  Start with the SGD home page:

  genome-www.stanford.edu/Saccharomyces

select "Search SGD", search for the gene name of interest.  The gene
name for the 18S rRNA is RDN18.  From the detail page on RDN18 select
"Gene/Sequence Resources".  On the Gene/Sequence Resources page you
will find many sequence analysis choices.  Two of interest for you
problem are "Restriction Fragment Sizes" at the bottom of the page.
This will provide a list of sizes for the particular DNA sequence.

For RDN18 you'll get:

EcoRI G'AATT_C

Cuts at:      0    1575    1800 
   Size:       1575     225
 

Both BamHI and HindIII are in the list of enzymes that do not cut that
sequence.

 Enzymes that do not cut: 

   BamHI  HindIII

You can also receive a graphic representation of the restriction map
from "Genome Restriction Map" which is in the "Sequence Analysis"
table.  We also provide "6-Frame Translation (with Restriction Map)"
which shows the DNA sequence, its translation (likely not of interest
in the RDN18 case), all annotated with restriction sites.

The Genome Restriction Map is created by SGD.  The other software is
the GCG software MAP and MAPSORT, provided with the permission of GCG
(www.gcg.com).

If you want to analysis a different region of the S. cerevisiae genome
select "Change Entered Selection or Coordinates" from the
"Gene/Sequence Resources" page.

Mike

J. Michael Cherry, Ph.D.         Internet: cherry at genome.stanford.edu
Department of Genetics           Stanford University School of Medicine
Medical Center, Room M341        Stanford, California  94305-5120
Voice: 650-723-7541              FAX: 650-723-7016

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