Whole-genome analysis of pseudorabies virus gene expression by real-time quantitative RT-PCR assay

Tombácz, Dóra; Tóth, Judit S; Petrovszki, Pál; Boldogkői, Zsolt

doi:10.1186/1471-2164-10-491

BMC Genomics

Table 3 Primer sequences^a

From: Whole-genome analysis of pseudorabies virus gene expression by real-time quantitative RT-PCR assay

Name^b	Forward primer sequence (5'-3')^c									Reverse primer sequence (5'-3')^d								Primer coordinates^e	Size of amplicon (bp)^f
*orf1*	GCC	TCG	TGT	TTC	TGA	TCC	TGC	TC		AAC	ACG	ACA	GAC	TCC	CGG	AGC	A	2204-2252	49
*ul54*	TGC	AGC	TAC	ACC	CTC	GTC	C			TCA	AAA	CAG	GTG	GTT	GCA	GTA	AA	2730-2795	66
*ul53*	CCA	AGG	CGC	TGT	ACC	TCT	G			TGT	GCC	GCT	CAT	AGT	GCA	G		3912-3977	66
*ul52*	CGC	GCA	ACT	TTC	ACT	TCC	ACG	CA		TGC	GCT	CGA	AGA	AGC	TCT	CGT	A	5325-5376	93
*ul51*	GCT	CAT	GCA	CCT	GTA	CCT	CTC	G		ACG	TCG	GAC	ATC	ACC	ACG	TTG	C	7989-8096	108
*ul50*	CTT	CTT	CGA	GGT	CTT	TGC	GC			ATG	TCG	TAT	CCG	GCG	TCC	T		8921-8971	51
*ul49.5*	TGA	CAT	TTT	ATA	TCT	GCC	TCC	TGG		TGC	AGC	ATC	CGG	GTG	C			9447-9525	79
*ul49*	CAT	CAC	CGT	GTG	CGA	G				CTT	TTC	CCT	TCC	GCC	CG			10247-10329	83
*ul48*	AGG	TGC	GGA	TCA	AGA	TGG	AG			CAG	TAC	GTG	TGG	TCG	CGG	T		11305-11359	55
*ul47*	GAG	CTC	ATG	GAC	GCG	CTC				CTG	GCG	CAT	GAC	GGC	GTC			13684-13767	84
*ul46*	TGC	TGT	GGT	CGA	CGT	TCG				TCT	GGG	CCT	TGT	GCT	TGA	A		14435-14494	60
*ul27*	ACT	ACG	AGG	ACT	ACA	ACT	ACG	TGC	G	GTC	ACC	CGC	GTG	CTG	ATC			17512-17575	64
*ul28*	GCG	CTC	TAC	TTT	GCG	GTG	GAG	AA		GAA	CTC	GCT	GAC	GCA	CCA	ATC	G	19781-19879	117
*ul29*	CTG	ATC	CTG	CGC	TAC	TGC	G			ACT	GCA	TCG	TGA	TCC	CCG			22609-22675	67
*ul30*	TCA	TCA	CGA	AGA	AGA	AGT	ACA	TCG	G	CCT	TCA	TGA	GCA	TCT	TGC	CG		27959-28015	57
*ul31*	GTG	GCA	GAC	CAT	GTT	CGT	GT			GGT	CTC	CCG	TCT	CCC	TTC	TT		28809-28859	51
*ul32*	TGC	TCA	GCT	ACT	CGG	AGA	ACA	AC		CAC	GGG	CTC	GAT	GCA	GTC			29841-29893	53
*ul33*	CGC	GCG	AGC	TGG	AAG	T				TGC	GTG	TGG	GCC	AGA	TAA			31031-31094	64
*ul34*	AGC	ACA	ACA	ACG	TGA	TCC	TGG			GAG	AGG	CTC	ATG	CCG	GTG			31696-31747	52
*ul35*	ATC	ATG	TCC	TTC	GAC	CCG	AAC			GAG	CGT	CTG	CGC	GGT	GA			32238-32288	51
*ul36*	CGT	CGG	TGG	GTA	TTA	GAG	ACC	A		GAA	CAA	GAG	CCA	TGG	ATT	TTC	G	34451-34501	51
*ul37*	CTA	CGA	CAT	GGA	CTT	TGT	GCA	GGA		AGT	TGG	TGT	GCT	GCG	CCA	CGT	A	44556-44611	56
*ul38*	CAC	CCG	GAA	CTC	GTG	CAT	GTA			CAG	AAG	AAA	CAC	TCC	TCC	CAC	G	46118-46273	156
*ul39*	GCT	GGC	CAA	GTT	CAA	GAC	G			CGC	ACA	TGT	CGA	TGA	GCA	G		48701-48759	59
*ul40*	GGA	CTT	TCC	CAT	GGC	GC				GCT	CGA	AAA	AGT	TGG	TGT	GCT	T	49802-49854	53
*ul41*	TGA	AGA	ACG	AGA	CGC	GGG				TGT	GTT	TCC	AAA	ACA	GGC	CC		50475-50525	51
*ul42*	GCT	CCC	CGA	GCG	TCG					CAT	GAT	GCA	GTA	GTC	GTT	GAA	CTC	52118-52173	56
*ul43*	CTG	GTG	CAG	GCG	TAC	GTG	A			GGA	TTT	AAT	GCT	AGT	GGC	GCA		53904-53954	51
*ul44*	TCG	TGA	GCA	GCA	TGA	TCG	T			GTC	GCC	ATG	ATG	ACC	AGC			55368-55437	70
*ul26*	TTC	TTC	CTC	GGC	GTC	GTC	AAC	TG		GTA	GTT	GCT	CAG	CAG	GTA	CAG	CA	56962-57087	126
*ul25*	GGC	AGT	TTG	GCG	TCT	CCA	G			CCA	GGC	AGA	GAA	AGT	ACA	GGA	GG	57336-57386	51
*ul24*	TGT	GCT	TCG	TCA	TCG	AGC	TC			TGG	GCG	TGT	TGA	GGT	TCC			59249-59305	57
*ul23*	ATG	ACG	GTC	GTC	TTT	GAC	CGC	CAC		CGC	TGA	TGT	CCC	CGA	CGA	TGA	A	59818-59898	81
*ul22*	GGC	GGC	CAT	CAC	CGT					GAG	AAT	AGC	CCT	CGG	AGG	AGA		62574-62647	74
*ul21*	TCA	GCT	GTT	TCG	GGC	GC				ATT	GAG	GAC	GAT	GGA	GAT	GTT	GG	64500-64551	52
*ul20*	GAG	AAC	GAC	GCG	CTG	CTG	AG			CAG	GAG	GCT	CAC	CAC	GTG			66226-66309	84
*ul19*	TCT	TTG	CGG	AGA	AGG	CCA	G			GCT	CTC	GGT	GCG	CGC				69841-69905	65
*ul18*	TGG	TGC	TGA	ACA	TGA	TCT	TCC			GGA	TGA	GCG	ACA	GCA	GGA	T		71443-71502	60
*ul17*	GGC	GTT	TTC	CTC	TTC	GAC	TAC	TAC		CAC	CCT	TAT	AAC	CTC	CCC	GC		74663-74713	51
*ul16*	CTG	TGG	CGC	CAG	GCG	GAC	AA			GAT	CTT	GCG	GCG	GGG	GAG	CAT	G	75670-75780	111
*ul15*	CAG	AAG	CAA	AAG	ACC	CCC	G			CGA	GTT	GAA	CTG	CTT	GAC	GAA	A	72204-72254	51
*ul14*	CGG	ACA	AGA	AAA	ACC	CCG	AG			CCT	GTT	TGG	CCG	CCA	TAA	A		77167-77217	51
*ul13*	AGC	CAC	CTG	GAC	GTC	AAG	G			CCA	TGA	GGC	TAA	AGT	CCC	CG		78083-78173	91
*ul12*	GCA	GAC	GGA	GAT	GCG	CTT				CCG	AGA	ACA	GGT	ACT	TGG	CG		79394-79449	56
*ul11*	ATG	GGA	CAG	TGT	TGC	TGC	C			TCA	AAG	TCC	TCG	AAC	GCG	T		80084-80178	95
*ul10*	CAT	TTT	GTG	TTT	CTC	GCC	CTC	TTT		ACC	CGT	GCC	CTT	GCA	GG			81390-81443	54
*ul9*	CAA	GTT	CAA	GCA	CCT	GTT	CGA			TGA	GGC	TGT	CGT	TGA	CGC			83337-83392	56
*ul8*	CCG	CTG	ATC	CTG	CCC	TG				GAA	GAT	GGG	CTC	CAT	GTG	G		86355-86405	51
*ul7*	TCC	GCG	GGT	TCG	CCT	TC				AGC	GAG	AGC	ACG	CGG	TC			87217-87271	55
*ul6*	CAG	GAG	CTG	ATC	CGC	TGC				TGT	TGG	AGT	ACG	AGA	CGG	ACA	C	87687-87765	79
*ul5*	TGG	ACA	TGG	CCA	CCT	ACG	T			ACC	GCG	CGA	TGG	TCA	T			91530-91592	63
*ul4*	GAG	CGA	GAC	CGA	CCA	TGA	C			TTA	TTT	CGT	AAA	ACG	AGT	AGG	CCA	91849-91899	51
*ul3.5*	CAA	CGG	AGC	ATC	AAC	GCC	TC			ATT	GAT	CGC	GGT	AGC	AAC	AGG	A	92478-92658	181
*ul3*	CTG	GGC	GCA	GCA	CGT					TCC	ACG	GAC	GCG	ACC	ATA			93502-93552	51
*ul2*	TTC	AGG	ACC	TGC	CCG	CAC	TTT	GGA		ACT	CAG	TCC	ACG	CTC	CAG	TCG	A	93914-93999	86
*ul1*	CTG	GTC	AAC	CCC	TTT	GTC	G			CGC	CTC	ATT	TAA	GGG	CTC	TC		94928-94987	60
*ep0*	GGG	TGT	GAA	CTA	TAT	CGA	CAC	GTC		TCA	GAG	TCA	GAG	TGT	GCC	TCG		96956-97006	51
*ie180*	CAT	CGT	GCT	GGA	CAC	CAT	CGA	G		ACG	TAG	ACG	TGG	TAG	TCC	CCC	A	103988-104056	69
*us1*	AGC	TCA	ACG	AGC	GCG	ACG	TCT	A		CGG	AAG	CTA	AAC	TCG	GAC	GCG	A	116466-116602	137
*us3*	GGG	CTT	TCC	TGA	TTT	ACA	AGA	TGT		AAG	GGC	GGC	GGA	CG				119245-119295	51
*us4*	ACC	TCG	ATC	TAC	ATC	TGC	GTC	G		GGC	CCT	GGT	GAT	CGC	CAT			120764-120850	87
*us6*	TGG	AAC	GAC	GAG	AGC	TTC	AGG			GTA	GAA	CGG	CGT	CAG	GAA	TCG		121690-121749	60
*us7*	CCC	GGG	AAG	ATA	GCC	ATG				AAG	AAG	ATC	AGG	AGG	ACG	ACG		123144-123199	56
*us8*	CTT	CGA	CGT	CTG	GTT	CCG	C			GGT	CAC	GCC	ATA	GTT	GGG	C		125136-125202	67
*us9*	CAG	GAC	GAC	TCG	GAC	TGC	TA			AGG	AAC	TCG	CTG	GGC	GT			125395-125453	59
*us2*	CGG	CTG	GAC	ACG	GAG	TG				AGT	TCA	GGT	ACT	GGA	TCC	CGT	T	126171-126222	52
*28S*	GGG	CCG	AAA	CGA	TCT	CAA	CC			GCC	GGG	CTT	CTT	ACC	CAT	T			54

^a This table shows the list of primer pairs used for analysis of PRV gene expression:
^b name of the primers
^cforward primer sequences
^dreverse primer sequences
^e Coordinates refer to the PRV genome sequence in strain Ka (NCBI Reference Sequence: NC_006151.1).
^fsize of the amplified products (amplicons) Underlined sequences were not available from strain Ka, and therefore we sequenced these DNA segments.

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ISSN: 1471-2164

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