Rapid single nucleotide polymorphism mapping in C. elegans

Davis, M Wayne; Hammarlund, Marc; Harrach, Tracey; Hullett, Patrick; Olsen, Shawn; Jorgensen, Erik M

doi:10.1186/1471-2164-6-118

BMC Genomics

Table 1 DraI SNP primers, locations and band sizes. In each pair of primers, the left primer is listed first; all primer sequences are given 5' to 3'. Interpolated genetic positions are from [9] release WS143.

From: Rapid single nucleotide polymorphism mapping in C. elegans

Genetic Location	Physical Location	Clone	N2 digest	CB4856 digest	Primers	Wormbase Identifier
I, -19	169, 017	F56C11	354, 146	500	ATGCCAGTGATAAGGAACGG	snp_F56C11 [4]
					TCACATCCCTTGTCGATGAA
I, -12	1,905,969	Y71G12A	503, 72	377, 126, 72	TCGAAATCAGGGAAAAATTGA	snp_Y71G12 [3]
					ACGATTTTCGGGGAGTTTTT
I, -6	2,818,973	W03D8	395, 144	538	GTTTTCACTTTTGCCGGTGT	pkP1052
					TGAAGGCGCATATACAGCAG
I, -1	4,594,014	D1007	325, 134, 41	459, 41	AAAATATCAGGAAAGAGTTTCGG	snp_D1007 [7]
					TTTAAAGATTAAGGGTGGAGCG
I, 5	10,722,146	B0205	494	365, 129	ATCTGGCACCAAATATGAGTCG	CE1-247
					AATCTCGATTTTCAAGGAGTGG	(rs3139013)**
I, 13	12,047,594	F58D5	445	295, 151	TCCTGGATAATCCCCAAAAA	snp_F58D5 [4]
					CCCTGCCATTGATCTTGTTT
I, 14	12,729,812	T06G6	236, 99, 78	335, 78	TTGAAATCCCCTTTAAAATCCC	uCE1-1361
					ACACTGGGTACCTGACTCATGC
I, 26	14,682,016	Y105E8B	360, 114, 27	474, 27	ATTATTAACGGCCACGGTGA	snp_Y105E8B [3]
					CCCACACACTCTCACCTTCA
II, -18	176,720	T01D1	263, 112	375	CCGAATTTTCAAATGGATGC	pkP2101
					CCATTGGAATTGCACACAAA
II, -14	2,121,018	R52	345	236, 109	CTGTGCTGTTGACGATATTGG	snp_R52 [5]
					ATGTCTCATTGCAAAATTCGG
II, -6	3,828,599	F54D10	516	387, 129	TTGTGAGCTTATATCTCAGTTGTCG	pkP2103
					AGATTTGGTTAGAAATATCACCGC
II, 1	9,052,466	T24B8	373, 121	494	TCAAAAACTTACAATCAATCGTCG	snp_T24B8 [1]
					CCAGAAAATCTGCACAGAAGG
II, 4	11,827,835	Y6D1A	224, 117, 124, 44	340, 124, 44	TTCTTCAAAAAGTCTAGGTTCAGCA	snp_Y6D1 [1]
					GGGGACGAAAACGGAGTTTG
II, 11	12,605,350	Y38E10A	483	352, 132	ACCGTTTAATAGGATTATTTGGG	uCE2-2131
					AAGTCTGCGGAATAATTGATGG
II, 16	13,235,564	F15D4	500	368, 132	TTCCAGGTAATACACATACAACTCC	pkP2116
					AAAAACACAAAGTTCAAAAACCC
II, 22	14,132,466	K09E4	365, 119	484	CCACTGGCTATAAGCTTTTCTAGG	CE2-215
					TAAGGATTTCAGGCTTTTAGGC	(rs3139227)**
III, -25	939,698	T12B5	206, 189	395	TATCATCGAAATCCCGGAAA	uCE3-637
					TTCGGACGGGAGTAGAATTG
III, -19	1,827,732	Y39A3CL	342, 78, 76	272, 78, 76, 70	TCCCAATTTCCCTCTAAAAACC	uCE3-735
					TTGAATTTGGACCATTTTGAGG
III, -12	2,599,699	Y71H2B	368, 105	473	GAGGAACCAAATCTGGCGTA	snp_Y71H2B [2]
					TGAAAACTTGGAAAATCGGTG
III, -7	3,359,033	F45H7	239, 85, 27	196, 85, 43, 27	AATTTGAATCAGTGACTTTTGGC	CE3-127
					TTTCTGCAAACATTTTTCTTCG	(rs3139272)**
III, -1	7,320,107	F56C9	486	354, 132	AAAAATACATGTCTACACAACCCG	snp_F56C9 [1]
					TTTCTTATCACTGTGCAGTCTTACC
III, 4	10,652,476	Y39A1A	355, 142, 30	497, 30	AGCGTTAAAGTATCGGTTATTTCG	snp_Y39A1 [9]
					TAAATTCATTTCAAACAATCGAGC
III, 12	11,656,188	Y41C4A	339, 156	495	ATCAAGTTTCTGATTGCTCTTTCC	snp_Y41C4 [2]
					AAAAACGTGATTTTTCAATTTTGC
III, +21	13,715,622	W06F12	273, 137, 78	200, 137, 78, 73	AGCAGGCTCACCATCATCATCA	uCE3-1426
					GACATTACGGTAGAGGAGATGGA
IV, -24	795,461	F56B3	301, 128, 71	429, 71	TGATGGTGTGTCTGCGTACC	uCE4-515
					AGAGCTGGAGAGCACGGATA
IV, -16	1,799,032	Y38C1BA	187, 304	491	CGCATAAATCCAACGTTCTCTG	snp_Y38C1B [2]
					AATCCATAAGTTTCGTGTTGGG
IV, -7	2,761,525	Y54G2A	498	250, 248	ACTCGGCATCCTCACGC	snp_Y54G2 [5]
					GTTGAAAATTTTTTCATAGCTATCATC
IV, -5	3,347,952	F42A6	295, 124	419	TGCTGAAATATTGGAAAATTGAGG	pkP4055
					TTATATCGTCGAGGAGGTTAGAGG
IV, 1	4,991,851	E03H12	376	300, 76	AAAATGGGAAGCGTACCAAA	pkP4071
					TGCTTGTAGCGTTTCCAAGA
IV, 8	13,049,020	F49E11	313, 77	390	GACACGACTTTAGAAACAACAGC	snp_F49E11 [1]
					TGGTATGGAGTCCCTATTTTGG
IV, 12	14,566,396	Y57G11B	284, 162, 52*	327, 119, 52*	TGTAAATACCCCACATTTCAAGC	snp_Y57G11B [2]
					AAATTTCCAATTGTTCAAAGCC	pkP4095*
IV, 14	16,085,085	Y105C5B	241, 108, 78, 48	319, 108, 48	TCGAATTGTTGTGTTTCTTTTGA	pkP4099
					TTCCAATTTTCTCGGTTTGG
V, -17	1,773,464	F36H9	307, 87, 79	386, 87	TTTCGGAAAATTGCGACTGT	pkP5076
					CGCGTTTTGGAGAATTGTTT
V, -13	2,726,662	C24B9	288, 167	455	TCATCTGTTATTTCGTCTCTTGC	uCE5-828
					CGGTAATAATATGCTTTGTGGG
V, -5	4,550,757	Y61A9LA	454	307, 147	GAGATTCTAGAGAAATGGACACCC	snp_Y61A9L [1]
					AAAAATCGACTACACCACTTTTAGC
V, 1	7,089,411	VC5	435, 70	300, 135, 70	AGAAATGATCCGATGAAAAAGC	pkP5097
					CCGATAGTGTTCATAGCATCCC
V, 6	13,951,850	R10D12	500	348, 152	CAAATTAAATATTTCTCAAAGTTTCGG	***
					ACATAAGCGCCATAACAAGTCG
V, 10	16,321,481	F57G8	475	288, 187	TAAAGCCGCTACGGAAATACTC	pkP5129
					ATTTTCTCCCTAATTCCAGGTG
V, 13	17,610,508	Y6G8	282, 205	487	CATTCATTTCACCTGTTGGTTG	uCE5-2609
					TCGGGAAGATAATCAAAATTCG
V, 18	18,782,547	Y17D7B	324, 164	488	GAAATTCAAATTTTTGAGAAACCC	snp_Y17D7B [3]
					TTCAGACCATTTTTAGAATATTCAGG
X, -17	2,065,464	F49H12	540	321, 219	ATATGTGAGTTTACCATCACTGGG	pkP6143
					ACGTTTTGAAAAATTTGGTTGC
X, -8	4,161,493	ZK470	422, 72, 40	326, 96, 72, 40	CCAAAACGGCCAAGTATCAG	pkP6105
					TTGCACTCTTTCTCCTTCCG
X, -4	5,934,688	C46F4	169, 54, 51, 35, 22	223, 51, 35, 22	AAGTGTTCAATGATTTTGTCTAATTG	uCE6-981
					TGACAGGAGAATACTTTTGAAGG
X, 2	10,637,922	F11A1	409, 133	542	AGCAACAAACAATGCAACTATGG	snp_F11A1 [2]
					TAAACAAGAGGGTACAAGGTATCG
X, 8	12,750,713	F22E10	341, 126	467	TTAAAACCATACAATTCTTCTCAGC	snp_F22E10 [1]
					GAATTCCCAATCAACAGAGAGC
X, 11	13,339,566	F46G10	318, 191, 37	509, 37	ACTGTTTACCGCGTCTTCTGC	pkP6132
					CCGTGTATATAAGAAAATGTGTTCG
X, 17	14,547,382	T24C2	409, 34	302, 107, 34	GCTGGGATTTTGAAGAGTTGTT	uCE6-1459
					CAGTGAATCATCCGTTGAATTT
X, 23	15,500,013	H13N06	358, 134	492	CAAATACCAAAGTTGATCGTGG	uCE6-1554
					TTGTTGCAATTAAATCAAACGG

*Y57G11B has two DraI SNPs within a single PCR product.
**dbSNP IDs are given where the SNP has been submitted to the NCBI dbSNP database [10].
***The SNP on R10D12 has not been added to wormbase. It can be found at [11]

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com