New SNP Table

Leonore Reiser lreiser at acoma.Stanford.EDU
Wed Dec 15 21:29:58 EST 1999



 TAIR is pleased to announce the Single Nucleotide Polymorphisms (SNPs)
 table at
	 http://arabidopsis.org/SNPs.html.

 This first set of SNPs was generously provided to us by Dr. Michael
 Mindrinos and includes the entire set of 412 SNPs described in Cho et
 al., Nat Genet 1999 Oct. 23(2):203-7. These SNPs have been given the
 additional prefix SGC- for the Stanford Genome Center. New SNPs will be
 added and given contributor-specific prefixes.

 THe sequences shown in the table have been confirmed by sequencing and
 HPLC to be polymorphic between the Col and Ler ecotypes. A subset of the
 SNPs that have been experimentally shown to distinguish between Col and
 Ler on oligonucleotide arrays are indicated by asterisks. Using BLAST we
 have located 286 of the SNPs to AGI clones on the TAIR sequence map
 (http://arabidopsis.org/cgi-bin/maps/Schrom) and sequence table
 (http://arabidopsis.org/cgi-bin/maps/Seqtable.pl).
 RI map positions for many of the SNPs will also be available shortly.

 The utility of the SNPs as markers may also be extended. Approximately
 30% of the SNPs should contain restriction site polymorphisms that can be
 used to develop CAPs markers. We will update the table with data on the
 restriction sites soon. Some polymorphic regions are deletions/insertions
 that may be useful in designing SSLP primers.

 Please let us know if you develop any of these SNPs into markers and we
 will update our Marker table.

 Please send your comments and questions to curator at arabidopsis.org

 -------------------------------------------------------------------------------
 Leonore Reiser                        	lreiser at stanford.edu
 The Arabidopsis Information Resource	FAX: (650) 325-6857
 Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
 Department of Plant Biology		URL: http://arabidopsis.org/
 260 Panama St.
 Stanford, CA 94305
 -------------------------------------------------------------------------------
 Note:  On September 1, 1999 AtDB was replaced by TAIR (The Arabidopsis
 Information Resource) at http://arabidopsis.org/  Please edit your AtDB
 bookmarks.  The AtDB website at http://genome-www.stanford.edu/Arabidopsis/
 will be phased out over the next few months.



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