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. |
||||||
|
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] |
||||||
|
Davis et al. BMC Genomics 2005 6:118 doi:10.1186/1471-2164-6-118 |
||||||
