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ARS nomenclature

Midori Harris midori at genome.stanford.edu
Thu Oct 19 19:07:49 EST 2000

Dear Colleagues,

As part of our efforts to annotate ARS sequences, SGD proposes using a
standardized nomenclature for ARSs. There is a naming convention that has
been used for ARSs on Chromosomes III and VI; it is described below
(courtesy of Dr. Carol Newlon):

  ARS elements should be named "ARS" followed by a series of 3 or 4
  digits, where the first 1 or 2 digits would identify the chromosome,
  and the last two digits would indicate the number of the ARS on that
  chromosome.  On chromosomes III and VI, the ARS elements have been
  numbered systematically from the left end to the right end.  For
  other chromosomes, which have not been systematically analyzed, our
  proposal was to name the ARS elements in the order of discovery, so,
  for example, the first ARS on chromosome I would be ARS101, etc.

Unless there are objections, SGD will follow this convention for ARSs
that are not repeated. For ARSs in subtelomeric repeats, we have
another proposal (which SGD received from Dr. Bik-Kwoon Tye):

  If coordinates for X and Y ARSs can be identified, then I would
  suggest (chromsome #, L/R for left/right telomere)-(# of class X or
  Y ARS counting most centromere proximal as 1).  So ARS 3LX1 would be
  an X ARS on chromosome 3, left telomere that is closest to the
  centromere.  ARS5RY would be Y ARS on chromosome 5, right telomere.
  You would not be able to distinguish one Y ARS from another because
  they are too conserved.

We hope to help the community agree on how to name subtelomeric ARSs,
so we welcome any comments.


 Midori Harris, Ph.D., Database Curator
 Saccharomyces Genome Database
 Stanford University Medical Center
 Department of Genetics
 Stanford, CA 94305-5120 USA
 phone: (650)725-8956  fax: (650)723-7016
 e-mail:   yeast-curator at genome.stanford.edu
 WWW:   http://genome-www.stanford.edu/


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