. 2016 Oct 5;16(6):705–715. doi: 10.1007/s10142-016-0522-z

Table 2.

SNP identification in promoter sequence of the pPAG2-L gene subfamily within BAC clones: CH242-60C13 and CH242-294016

SNP localization in 1204-bp promoter				BAC clones (Duroc)				Crossbreeds
SNP locus (IUPAC code)^b		SNP locus acc. DNASIS^c	pPAG2	CH242-60C13^d		CH242-294016^e
SNP locus (IUPAC code)^b		SNP locus acc. DNASIS^c	pPAG2	Amplicon 1	Amplicon 2	Amplicon 3	Amplicon 4
F1 region
1)	g.-101 -102Ins G	g.1100_1101InsG	DelG	GG	–/–	GG	–/–	GG
2)	g.-168C ≥ T(Y)	g.1033C>T	CC	TT	–/–	TT	–/–	CC
3)	g.-316A ≥ G(R)	g.886 A>G	AA	AG	–/–	AG	–/–	GG/AG
4)	g.-417C ≥ A(M)	g.785C>A	CC	AC	–/–	AC	–/–	AA
F2 region
5)	g.-740G>T(K) ^a	g.462G>T	GG	GG	TT	GG	TT	GG
6)	g.-810A>G(R) ^a	g.392A>G	AA	AA	GG	AA	GG	AA
7)	g.-820C ≥ A(M)	g.382C>A	CC	AC	CC	AC	CC	AA/CC
8)	g.-826G>A(R) ^a	g.376G>A	GG	GG	AA	GG	AA	GG
9)	g.-827G>C(S) ^a	g.375G>C	GG	GG	CC	GG	CC	GG
10)	g.-828G>A(R) ^a	g.374G>A	GG	GG	AA	GG	AA	GG
11)	g.-836C>A(M) ^a	g.366C>A	CC	CC	AA	CC	AA	CC
12)	g.-839G>A(R) ^a	g.363G>A	GG	GG	AA	GG	AA	GG
13)	g.-870T>G(K) ^a	g.332T>G	TT	TT	GG	TT	GG	TT
14)	g.-890C>T(Y) ^a	g.312C>T	CC	CC	TT	CC	TT	CC
15)	g.-924G ≥ A(R)	g.278G>A	GG	GG	AA	GG	AA	GG
16)	g.-929A ≥ T(W)	g.273A>T	AA	AA	TT	AA	TT	AA
17)	g.-931A ≥ C(M)	g.271A>C	AA	AA	CC	AA	CC	AA
18)	g.-950DelA ^a	g.252DelA	AA	AA	DelA	AA	DelA	AA
19)	g.-956DelG ^a	g.246DelG	GG	GG	DelG	GG	DelG	GG
20)	g.-968A ≥ C(M)	g.234A>C	AA	AC	CC	AC	CC	AC/CC
21)	g.-973G>A(R) ^a	g.229G>A	GG	GG	AA	GG	AA	GG
22)	g.-974DelG ^a	g.228DelG	GG	GG	DelG	GG	DelG	GG
23)	g.-975DelG ^a	g.227DelG	GG	GG	DelG	GG	DelG	GG
24)	g.-976DelG ^a	g.226DelG	GG	GG	DelG	GG	DelG	GG
25)	g.-977G>T(K) ^a	g.225G>T	GG	GG	TT	GG	TT	GG
26)	g.-978G>T(K) ^a	g.224G>T	TT	TT	GG	TT	GG	TT
27)	g.-981C ≥ G(S)	g.221C>G	CC	CC	GG	CC	GG	CG
28)	g.-982T ≥ G(K)	g.220T>G	TT	TT	GG	TT	GG	TG
29)	g.-983T ≥ C(Y)	g.219T>C	TT	TT	CC	TT	CC	CT
30)	g.-984T ≥ A(W)	g.218T>A	TT	TT	AA	TT	AA	AT
31)	g.-985G ≥ T(K)	g.217G>T	GG	GG	TT	GG	TT	GT
32)	g.-986T ≥ C(Y)	g.216T>C	TT	TT	CC	TT	CC	AT
33)	g.-990C ≥ G(S)	g.212C>G	CC	CC	GG	CC	GG	CG
34)	g.-1024T ≥ C(Y)	g.178T>C	TT	CT	CC	CT	CC	CT
35)	g.-1029A ≥ G(R)	g.173A>G	AA	AG	GG	AG	GG	AG
36)	g.-1042C>A(M) ^a	g.160C>A	CC	CC	AA	CC	AA	CC
37)	g.-1060C>T(Y) ^a	g.142C>T	CC	CC	TT	CC	TT	CC
38)	g.-1070G>A(R) ^a	g.132G>A	GG	GG	AA	GG	AA	GG
39)	g.-1077C>T(Y) ^a	g.125C>T	CC	TT	–/–	TT	–/–	CC
40)	g.-1093G>A(R) ^a	g.109G>A	GG	AA	–/–	AA	–/–	GG
41)	g.-1095G>T(K) ^a	g.107G>T	TT	GG	–/–	GG	–/–	TT
42)	g.-1096C>A(M) ^a	g.106C>A	CC	AA	–/–	AA	–/–	CC

SNPs occur in Duroc and crossbreed pigs are underlined

^aSNPs not detected in crossbreed pigs are italicized

^bNumbering of SNPs submitted in dbSNP/NCBI database

^cNumbering according to promoter sequence U39198, GenBank (Szafranska et al. 2001)

^dBAC clone (CH242-294016) containing pPAG3 gene sequences

^eBAC clone (CH242-60C13) containing pPAG3 and pPAG6 gene sequences