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).
From: The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation
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 |