Wheat SNP Assay record - 11/6/02

Wheat SNP assay name : 120_001 (provisional name)
Other names : X15232_1257_6BS
Gene family match : cytosolic phosphoglycerate kinase (EC 2.7.2.3)(see : X15232)
Map position : 6BS, centromeric (Opata x Synthetic)
Last update : Thu, Jun 6, 2002 at 17:28
Data source : Somers/Contig120/Issue01/ April2002
Test designed by : Agrogene, pete.i@agrogene.com
Allele description : 89 (T) and 92 (A) bases; corresponds to position 1257 in sequence X15232
Date Allocated : 22.4.02
Date Report Returned : 30.4.02
PCR comments: 25ul volume, ampliTaq Gold enzyme, annealing temperature 60C-55C touchdown, 3 cycles/degree, then 30 cycles at 55C. Resolution conditions: Acrylamide sequencing gel or automated sequencer - length difference of 3 bases between alleles. Primers tested, test OK.
General comments: Original contig split into 3 regions, this was derived from the alignment most 3' in gene. Reverse primer exploits 2 closely linked SNPs. Last base of forward primer is thought to be locus specific. Tms and parameters calculated by Primer Express 1.5
Images: 00160-001.GIF
Alignment file : 120capOut.txt
FastA File : Contig120

Locus specific primer details
Name	W00120_001LF
Seq.	CGACAAAATGAGCCACATTTCC
Len.	22
Tm.	60
Strand	F------->

SNP allele 1 primer details
Name	W00120_001TR	from sequence : TaE05012C08F
Seq.	CGTCAAGGGCAAAAACACCA	GGATGTTGGC CCAGATTCCA TCAAGACTTT TGCAGAAGCC TTGGACACCA 50 CCAAGACTGT TATCTGGAAC GGTCCTATGG GAGTCTTTGA GTTTGAGAAG 100 TTTGCCGCAG GCACTGATGC GATCGCGAAG CAGTTGGCTG AGCTTACTGG 150 GAAGGGTGTC ACGACCATCA TTGGTGGAGG TGACTCCGTT GCTGCTGTTG 200 AAAAGGCTGG GCTGGCCGAC AAAATGAGCC ACATTTCCAC CGGCGGTGGC 250 GCGAGCTTGG AGCTGCTGGA AGGCAAGCCC CTCCCTGGTG TTTTTGCCCT 300 TGACGAGGCG TAGGTTGATT CGGTTTCACC TATCAGCTTG CTGCGTGCCC 350 CTTTTGTTTG GGATTTCATC TCGGTGTAAC GCTGGAACGT TATATGTCCC 400 AAGGAAACTT TGAGATAGGC TTGTCGCCAA TTTTTGCTAG TAGATGAGTC 450 GTGAATAATT ATCAACTTCC TCTGTGGGTG TGAAGTGATG TGGCTGGAAT 500 TTAACGTACC CCTGTGGATG TGTATGGTTT T 531
Len.	20
Tm.	60
Strand	<-------R
PCRSize	89
Symbol	T

SNP allele 2 primer details
Name	W00120_001AR	from sequence : CHB0068_H09_O18Z_076
Seq.	CCTCTTCAAGGGCAAGAACACCT	AGTTTGAGAA GTTCGCCGCA GGCAGTGATG CGATCGCCAA GCAGTTGGGT 50 GAGCTTATTG GGAAGGGTGT CATGACCATC ATTGGTGGAG GTCACTCTGT 100 TGCCGCTGTT AAGAAGCCTG GGCTGGCCGA CAAGATGAGC CACATTTCCA 150 CCGGCGGTGG CGCGAGCTTG TAGCTGTTGG AAGGCAAGCC CCTCCCAGGT 200 GTTCTTGCCC TTGAAGAGGC GTAGGTTGAT TCGGTTTCAC CTATCAGCTT 250 GGTGCGTGCA CCTTTTGTTT GGGATCTCAT CTCGGTGTAA CGCCGGAGAC 300 GTTATATGTC CCAAGGAAAC TTTGAGATAG GCTTGTCGCC AATTTTTGGT 350 AGTACATGAG TCGTGAATAA TTA 373
Len.	23
Tm.	60
Strand	<-------R
PCRSize	92
Symbol	A

Scores of standard genotypes:

Chinese_Spring	A/T
Opata	A
Soisson	A
Synthetic	T