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translation start site re-annotation

Dianna Fisk fisk at genome.stanford.edu
Tue Sep 23 14:55:08 EST 2003

Dear Colleagues,

As you are all most likely aware, there has been an explosion in the
availability of fungal genomic sequences. Several groups have recently
published re-analyses of S. cerevisiae annotations based on ORF
conservation among different fungal species. SGD has examined these
data and has re-annotated the start site methionine codons for 77
different S. cerevisiae open reading frames. The numbering for both
the nucleotides in the DNA coding sequence and the amino acids in the
predicted protien have been changed accordingly. In all cases, the
original start codon is not conserved or is not in frame in orthologs
from other Saccharomyces species, while the new start codon is a
conserved, downstream ATG that is in frame with the previously
annotated start.

In making these changes, SGD relied heavily upon the work of Kellis et
al. (Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003)
Sequencing and comparison of yeast species to identify genes and
regulatory elements. Nature 423(6937):241-54) and Cliften et al.
(Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J,
Waterston R, Cohen BA, Johnston M (2003) Finding functional features
in Saccharomyces genomes by phylogenetic footprinting. Science
301(5629):71-6). However, each change proposed by either of these
groups was individually reviewed by an SGD curator. Work done by other
sequencing groups and published experimental data were taken into
consideration before incorporating the proposed changes.

You can find a tables of the changes at the following URLs:


Best Regards,


  Dianna Fisk, Ph.D., Database Curator
  Saccharomyces Genome Database
  Stanford University Medical Center
  Department of Genetics
  Stanford, CA 94305-5120 USA
  phone: (650)498-6004  fax: (650)723-7016
  email:  fisk at genome.stanford.edu

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