Table 1

*Oligonucleotides for sequencing and genotyping Prnp* alleles**
Primer number^a	DNA sequence^b	Gene region	Orientation	Function	T_m(°C)	STS length (bp)	Termination mixture	Mass (Daltons)	Codons 210/211^c

67661	gac att aga atc act tcc ata gg	Intron 2, CDS, 3' UTR	Sense	Amplification, sequencing	58	1498	-^d	-	-
65547	ata ctg agc taa cgg gac tt	Intron 2, CDS, 3' UTR	Antisense	Amplification, sequencing	58	1498	-	-	-
65617	gat ttt tac atg ggc ata tga	Intron 2, CDS, 3' UTR	Sense	Amplification, sequencing	60	985	-	-	-
42618	gcc aag ggt att agc ata ca	Intron 2, CDS, 3' UTR	Antisense	Amplification, sequencing	60	985	-	-	-
42642	cct gga ggc aac cgt tat	CDS	Sense	Sequencing	62	-	-	-	-
27774	ctc ctg cca cat gct tca t	CDS	Antisense	Sequencing	62	-	-	-	-
58117	tac agg cca gtg gat cag ta	CDS	Sense	Amplification	60	203	-	-	-
58119	gcc cct cgt tgg taa taa	CDS	Antisense	Amplification	60	203	-	-	-
58118	acg ttg gat gta cag gcc agt gga tca gta	CDS	Sense	Amplification for hME (with mass tag)	60	226	-	9311.10	-
58120	tgg acg ttg gat ggc ccc tcg ttg gta ata a	CDS	Antisense	Amplification for hME (with mass tag)	60	226	-	9582.20	-
58141	caccaagggggagaacttcac-C-G-aaactgacatcaagatgat	CDS	Sense	control template for cE211 allele	93	-	-	12958.40	-
58142	atcatcttgatgtcagttt-C-G-gtgaagttctcccccttggtg	CDS	Antisense	control template for cE211 allele	93	-	-	12868.30	-
64161	caccaagggggagaacttcac-T-G-aaactgacatcaagatgat	CDS	Sense	control template for tE211 allele	93	-	-	12973.50	-
64162	atcatcttgatgtcagttt-C-A-gtgaagttctcccccttggtg	CDS	Antisense	control template for tE211 allele	93	-	-	12852.30	-
58143	caccaagggggagaacttcac-C-A-aaactgacatcaagatgat	CDS	Sense	control template for cK211 allele	93	-	-	12942.40	-
58144	atcatcttgatgtcagttt-T-G-gtgaagttctcccccttggtg	CDS	Antisense	control template for cK211 allele	93	-	-	12883.30	-
58145	caccaagggggagaacttcac-T-A-aaactgacatcaagatgat	CDS	Sense	control template for tK211 allele	93	-	-	12957.50	-
58146	atcatcttgatgtcagttt-T-A-gtgaagttctcccccttggtg	CDS	Antisense	control template for tK211 allele	93	-	-	12867.30	-
62792	caa ggg gga gaa ctt cac	CDS	Sense	hME primer	58	-	ddA^e	5557.60	-
-	caa ggg gga gaa ctt cac ca	CDS	Sense	CA allele analyte	-	-	ddA	6144.00^f	cK211
-	caa ggg gga gaa ctt cac ta	CDS	Sense	TA allele analyte	-	-	ddA	6159.00^f	tK211
-	caa ggg gga gaa ctt cac cga	CDS	Sense	CGA allele analyte	-	-	ddA	6473.20^f	cE211
-	caa ggg gga gaa ctt cac tga	CDS	Sense	TGA allele analyte	-	-	ddA	6488.20^f	tE211
58148	atc atc ttg atg tca gtt t	CDS	Antisense	hME primer	49	-	ddC/ddG^e	5783.80	-
-	atc atc ttg atg tca gtt tc	CDS	Antisense	C allele analyte	-	-	ddC/ddG	6057.00	nE211
-	atc atc ttg atg tca gtt ttg	CDS	Antisense	TG allele analyte	-	-	ddC/ddG	6401.20	cK211
-	atc atc ttg atg tca gtt tta g	CDS	Antisense	TAG allele analyte	-	-	ddC/ddG	6714.40	tK211

^aUSMARC primer number; GenBank Accession number AY335912 ^bPrimer sequences are listed 5' to 3'; primers 58118 and 58120 are analogous to primers 58117 and 58119, respectively, but with additional nucleotides on the 5' end (5'-acgttggatg-3' and 5'-tggacgttggatg-3', respectively) to shift their masses out of the analyte range. ^cnE211 refers to either cE211 or tE211 since the genotype for this analyte is ambiguous in the antisense direction. ^dNot applicable. ^eMixture also contains the complement dNTPs. ^fAlthough a conservative hME assay design includes 40 Dalton spacing between analytes, only 15 Dalton spacing was possible in this case. Nevertheless, the typical instrument resolution of approximately 4 Daltons is sufficient to resolve these analytes.
Heaton et al. BMC Veterinary Research 2008 4:25 doi:10.1186/1746-6148-4-25