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. 2006 Jul 21;7:185. doi: 10.1186/1471-2164-7-185

Table 2.

5' genome location (according to rCRS) and primer sequences for 36 primers including 34 (#3–36) used to amplify formalin fixed, paraffin embedded tissue. Primers in bold (1, 2) indicate chromosome (Chr) 17 specific primers redesigned to capture rest of D-loop fragment. The region spanned by 15971–16410 was split into two separate amplicons for the ρ 0 amplification (15673–16009 and 15777–16398).

Primer Sequence (5'-3') Mitochondria Position Chr Accession Number Nuclear Position
1 16319F ATC GCT CAT GGT AGA TAG CAC 16319-446 17 NT_024862.13 337395–338087
446R TGT TAG TTG AGG GGT GAC TGTT
2 374F AAT CCA ACT CAA CCA GAG CCC A 371–461 17 NT_024862.13 338011–338101
781R TGA GCT GCA CTA ATG CGT GC Nuclear Gap 17 NT_024862.13 338102–338279
574–783 17 NT_024862.13 338280–338489
3 615F ATG TTT AGA CGG GCT CAC ATC ACC 651–1247 11 NT_009237.17 9318994-9318400
1247R CAA GAG GTG GTG AGG TTG ATC G
4 1051F ACA ATA GCT AAG ACC CAA ACT GGG AT 1062–1639 11 NT_009237.17 9318585-9318008
1644R CTC CTA AGT GTA AGT TGG GTG CTT TG 1068–1618 5 NT_006713.14 30541827-30541277
5 1488F CGT CAC CCT CCT CAA GTA TAC TTC 1497–2049 11 NT_009237.17 9318150-9317598
2084R TAC AAG GGG ATT TAG AGG GTT CTG TG 1497–2049 5 NT_006713.14 30541398-30540846
1497–2049 3 NT_005612.14 2832399-2832340
6 1938F AGA GCA CAC CCG TCT ATG TAG CAA 1938–2612 11 NT_009237.17 9317709-9317035
2612R GGA ACA AGT GAT TAT GCT ACC TTT GCA C 1938–2612 3 NT_005612.14 2831958-2831284
1939–2612 17 NT_024862.13 339611-340281
1940–2612 8 NT_023678.15 902509-901844
1971–2612 5 NT_006713.14 30540924-30540284
7 2417F CAC TGT CAA CCC AAC ACA GGC AT 2402–3078 20 NT_011362.9 20987219-20986564
3101R TAG AAA CCG ACC TGG ATT ACT CCG 2417–3076 17 NT_024862.13 340090-340749
8 3021F CGC TAT TAA AGG TTC GTT TGT TC 3070–3673 17 NT_024862.13 340743-341346
3695R ATC AGG GCG TAG TTT GAG TTT G
9 3230F GTT AAG ATG GCA GAG CCC GGT AA 3253–3859 4 NT_016354.17 80880160-80879559
3893R GTT CGG TTG GTC TCT GCT AGT GT 3253–3870 2 NT_005058.14 9588111-9587524
3296–3870 16 NT_037887.4 3360917-3360343
3323–3870 X NT_011630.14 2761822-2761281
3347–3870 17 NT_024862.13 341020-341543
10 3728F CAT ATG AAG TCA CCC TAG CCA TC 3814–4391 17 NT_010718.15 19103293-19103865
4417R TTT AGC TGA CCT TAC TTT AGG ATG GG 3816–4391 17 NT_024862.13 341489-342064
11 4337F ATG AGA ATC GAA CCC ATC CCT GAG 4361–5010 1 NT_077913.2 43543-44192
5035R CAT CCT ATG TGG GTA ATT GAG GAG T
12 4867F GAC AAA AAC TAG CCC CCA TCT CAA 4866–5554 1 NT_077913.2 44048–44736
5646R GCT TAA TTA AAG TGG CTG ATT TGC GT 5169–5632 2 NT_005403.15 62851661-62852120
13 5468F CAC GCT ACT CCT ACC TAT CTC 5508–6124 17 NT_024862.13 343174–343794
6145R CAG TTG CCA AAG CCT CCG ATT ATG 5511–6121 1 NT_077913.2 44693–45303
14 5867F CAA TGC TTC ACT CAG CCA TTT TAC C 5892–6481 1 NT_077913.2 45074–45663
6482R GAC TGC TGT GAT TAG GAC GG
15 6418F AAC CCC CTG CCA TAA CCC AAT AC 6441–7056 1 NT_077913.2 45623-46239
7082R GAA GCC TCC TAT GAT GGC AAA TAC AG
16 6911F TGC AGT GCT CTG AGC CCT AGG ATT 6914–7521 1 NT_077913.2 46097-46704
7554R CTT TGA CAA AGT TAT GAA ATG GTT TTT CTA ATA 6935–7521 5 NT_034772.5 1804907-1804321
17 7400F CCC ACC CTA CCA CAC ATT CGA A 7453–8005 1 NT_077913.2 46636–47188
8029R GGC TTC AAT CGG GAG TAC TAC TCG
18 7829F CGC ATC CTT TAC ATA ACA GAC GAG G 7853–8472 1 NT_077913.2 47036–47622
8441R GTT GGG TGA TGA GGA ATA GTG TAA GG
17 8346F CAACACCTCTTTACAGTGAAATGCCC 8471–8941 1 NT_077913.2 47652–48122
8959R CGATAATAACTAGTATGGGGAT
20 8814F CCA ACT ATC TAT AAA CCT AGC C 8814–9427 1 NT_077913.2 47995–48594
9413R GCC TTG GTA TGT GCT TTC TCG TGT 8816–9375 5 NT_034772.5 1803025-1802466
21 9247F GCC CAT GAC CCC TAA CAG G 9268–9845 5 NT_034772.5 1802573-1801994
9868R CGG ATG AAG CAG ATA GTG AGG 9545–9859 7 NT_079592.1 56744603-56744909
22 9711F CTG GGT CTC TAT TTT ACC CTC C 9730–10300 5 NT_034772.5 1802112-1801539
10285R GGT AGG GGT AAA AGG AGG GCA
23 10198F CCC GCG TCC CTT TCT CCA T 10206–10768 5 NT_034772.5 1801633-1801071
10766R TTA GCA TTG GAG TAG GTT TAG G
24 10696F CCC TAC TAG TCT CAA TCT CCA A 10694–11509 9 NT_008470.17 2194293–2194999
11426R CTT CGA CAT GGG CTT TAG GGA G 10751–11426 5 NT_034772.5 36678748-36678073
25 11210F TTC TAC ACC CTA GTA GGC TCC CTT 11234–11786 5 NT_034772.5 36678265-36677713
11813R GTA GAG TTT GAA GTC CTT GAG AGA GG
26 11629F AAT CAG CCA CAT AGC CCT CGT AG 11651–12205 5 NT_034772.5 36677848-36677294
12231R GTT AGC AGT TCT TGT GAG CTT TCT CG 11841–12206 5 NT_034772.5 1799998-1799633
27 12096F TCC TAT CCC TCA ACC CCG ACA T 12118–12681 5 NT_034772.5 36677381-36676818
12709R GGA AGA TGA GTA GAT ATT TGA AGA ACT G
28 12528F GAA CTG ACA CTG AGC CAC AAC C 12550–13070 5 NT_034772.5 1799289-1798769
13096R CAA CTA TAG TGC TTG AGT GGA GTA GG
29 12882F CAT CCT CGC CTT AGC ATG ATT TAT CC 12908–13493 5 NT_034772.5 36676591-36676006
13516R GGT CTT TGG AGT AGA AAC CTG TG 12908–13493 5 NT_034772.5 1798931-1798346
30 13239F CGT AGC CTT CTC CAC TTC AAG TC 13262–13827 5 NT_023148.12 2217633-2218198
13851R GTT GAG GTC TAG GGC TGT TAG AAG
31 13354F TTT ATG TGC TCC GGG TCC ATC AT 13377–13935 5 NT_023148.12 2217748-2218306
13957R CTA GAT AGG GGA TTG TGC GGT G
32 13838F CCC TAG ACC TCA ACT ACC TAA CC 13895–14454 5 NT_023148.12 2218266-2218823
14458R GAT GGC TAT TGA GGA GTA TCC T 14324–14535 5 NT_034772.5 36675175-36674964
33 14339F ACC CCA TCA TAC TCT TTC ACC C 14550–15042 5 NT_034772.5 1797288-1796796
15052R TAG GCC TCG CCC GAT GTG TA 14604–15051 5 NT_034772.5 36674895-36674448
34 14971F TGG CTG AAT CAT CCG CTA CCT T 15041–15785 17 NT_024862.13 336116-336858
15786R AAA GGG TAG CTT ACT GGT TGT CC 15345–15774 5 NT_023148.12 2219715-2220144
35 15673F ATC CAA ACA ACA AAG CAT AAT ATT TC 15672–15994 5 NT_023148.12 2220042-2220364
16009R AAT TAG AAT CTT AGC TTT GGG TG
36 15777F GCT ACC CCT TCA TCA CCT TC 15785–16388 17 NT_024862.13 336858-337463
16398R CAA CGG ACC ACT ATC TGA GGG