Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs

Table 3 Cross-species amplification results for 50 primer pairs with no IS-mismatches

Gene	Hum^a	Mon	Dog	Cat	Hor	Cow	Goa	Pig	Ham	Rat	Mou	prot id^b	GC^c	Notes^d
PTBP2	4 ^e	4	4	4	4	4	4	4	4	4	4	99	32.8^c
HAT1	4	4	4	4	4	4	4	4	4	4	4	93	39.6
PTPRU	4	4	4	4	4	4	4	4	4	4	4	95	54.8
MACF1	4	4	4	4	4	4	4	4	4	4	4	78	37.8
FRAP1	4	4	4	4	4	4	4	4	4	4	4	99	39.9
LRP1B	4	4	3	4	3	4	4	4	4	4	4	91	39.5
LYST	4	4	4	3	3	4	4	4	4	4	0	84	28.6
HNRPU	4	4	4	2	4	4	4	4	4	4	4	94	39.6
SLC20A1	4	4	4	2	4	4	4	4	4	4	4	90	39.4
RND3	4	4	0	4	4	4	4	4	4	4	4	100	51.6
CDC7	4	2	4	4	4	4	4	4	2	4	0	81	33.6
PABPC4	4	4	4	4	4	4	4	4	3	2	2	95	51.2
NR4A2	4	4	4	3	0	4	4	4	4	4	4	99	43.9
KYNU	3	4	4	3	4	4	4	0	4	4	4	85	30.5
DDX18	4	4	0	3	4	4	4	4	4	4	4	85	39.4
CLCN6	4	4	4	4	4	0	4	3	3	4	4	96	52.7	1^d
PSCDBP	4	4	3	4	4	0	4	3	4	4	4	81	37.4
ABCA4	4	4	2	4	4	4	4	2	3	2	3	88	53.5
MDH1	4	4	4	4	4	4	2	2	4	2	4	96	39.5
ADD2	4	4	0	4	4	4	2	4	2	4	4	94	51.9
CTNNA2	4	4	4	4	4	0	0	4	3	4	4	98	45.6
SLC1A4	4	4	4	4	2	2	4	2	2	3	4	89	51.8
LAMC1	4	4	4	4	0	4	4	0	4	2	4	92	37.9
FASLG	4	4	4	2	4	4	4	4	0	0	0	77	40.1
HK2	2	4	4	4	3	0	3	0	4	4	4	94	46.5	2
ORC4L	3	3	3	4	3	3	3	0	3	4	3	88	33.2
CCT7	2	4	2	2	1	4	4	4	2	2	4	95	46.2	2
FLVCR	4	4	4	4	4	0	4	1	0	4	0	77	39.0	1
ITGAV	4	4	0	4	4	4	4	4	0	0	0	91	36.4
MYO1B	4	4	4	4	0	0	0	4	4	4	4	89	31.5
RGS16	4	4	1	4	3	4	4	4	0	0	0	84	44.7
PINK1	4	4	0	2	4	3	1	1	4	4	4	81	48.9
EIF5B	4	4	4	4	3	0	0	4	3	1	4	75	38.7	1
GNB1	3	4	4	4	4	0	3	0	3	0	3	100	51.6
GDAP2	4	4	3	4	0	0	0	3	4	4	4	94	35.0
BIN1	0	3	3	3	0	3	3	3	0	3	3	69	60.8	3
WDR8	4	4	4	4	0	0	0	0	4	4	4	89	35.0
AP4B1	4	4	4	0	4	0	0	0	3	4	4	90	39.0
CYP2J2	4	4	1	4	3	3	0	2	0	2	0	76	43.7	1
GABRD	0	1	2	2	1	2	2	0	4	4	4	91	64.0	3
SULT1C1	4	4	4	4	4	0	0	0	0	2	0	83	45.9	1
RBBP4	2	2	2	2	2	2	2	0	2	2	2	99	38.8	2
DVL	0	0	4	2	2	2	2	0	2	2	4	95	69.6	3
SAC	4	0	0	4	4	0	0	0	4	4	3	73	45.0
CCNT2	0	0	0	4	0	0	0	4	4	4	4	69	54.6	3
JAK1	4	0	0	4	0	0	3	4	4	0	4	93	52.4
TBR1	0	3	0	2	0	1	1	2	3	3	3	99	53.4	3
WDR39	1	0	0	2	1	0	1	0	3	4	4	94	54.1	3
ARID4B	1	3	0	0	0	0	0	0	3	3	1	87	35.7	3
STAT1	0	3	0	0	0	0	0	0	0	4	4	92	39.9	4

^aBoxes indicate index species used to design primers. Species abbreviations are: Hum, human; Mon, monkey; Hor, horse; Goa, goat; Ham, hamster; Mou, mouse.
^aThese numbers are the percent protein sequence identity between human and mouse.
^cThese numbers are the G + C content in the e-PCR amplified human product.
^dNotes: 1, rabbit was the second index species for these primer pairs, except FLVCR, for which cat was used; 2, one or more processed pseudogenes apparent in the human genome; 3, contains a > 130 bp window in amplified human product with > 59% G + C; 4, strong primer-dimer seen in amplifications.
^eNumbers 0–4 correspond to amplification rankings as exemplified in Fig. 1.

ISSN: 1471-2164