Oligonucleotide Primers - Nuclear Genome

By placing these primer sequences on the web, I am making them available for general use. Thus, you have my permission to use these sequences and order primers for your own use. Some of the primers here have not been published in the literature. For those that have, please see references listed at end for proper citation. Given the low cost of primers these days, I prefer that you do not request aliquots of these (except under special circumstances).

Small Subunit (SSU) rDNA

Name Primer Sequence 5'-3' Length Position on Glycine Comments Ref.
23 for TTG GTT GAT CCT GCC AGT AG 20 4- 24 replaces 25e 2
12 for TCC TGC CAG TAS TCA TAT GC 20 12 - 21
366 for GTC TGC CCT ATC AAC T 16 307-322 1st G mism. 2
530 for GTG CCA GCM GCC GCG G 16 566-581 2
530 for GTG CCA GCA GCC GCG G 16 566-581
561 for GTG CCA GCA GCC GCG G 16 566-581
700e for YAG AGG TGA AAT TCT TGG 18 901-918 2
922 for GAA ACT TAA AKG AAT TG 17 1134-1150 2
1322 for TAA CGA ACG AGA CCT CAG CCT 21 1322-1342 2
1453 for ARC TTC TTA GAG GGA C 16 1378-1393 2
1406 for TGY ACA CAC CGC CCG T 16 1633-1648
1631 for TTT GTA CAC ACY GCC CGT CG 20 1631-1650 2
1830 for AAC AAG GTT TCC GTA GGT GA 20 1769-1787 7
NTS-1 rev GAG ACA AGC ATA TGA CTA C 19 20-48
32 rev GCT ACG TTC TTC ATC GAT GC 20 32-52
79 rev GAT GGT TCA CGG GAT TCT GC 20 32-52
145 rev CTA GYA TTR CTA CGG TTA TCC 21 141-161 1, 2
310 rev CCA TCG AAA GTT GAT AGG GCA 21 310-330 2
428 rev TTT CTC AGG CTC CCT CTC CGG 21 385-405 1, 2
567 rev AAT TAC CGC GGC TGC TGG CA 20 567-586 2
626 rev TCC AAC TAC GAG CTT 15 626-640 1, 2
854 rev ATC ATT ACT CCG ATC CCG 18 847-864 1, 2
905 rev AAT CCA AGA ATT TCA CCT CT 20 905-925 2
1131 rev CAA TTC CTT TAA GTT TCA GCC 21 1130-1150 2
1324 rev AAG AAC GGC CAT GCA CCA CC 20 1269-1288 1, 2
1433rev ATC TAA GGG CAT SAC AGA CC 20 1433-1452 2
1575 rev CTC GTT GAA GAC CAA CAA 18 1562-1579 1, 2
1769 rev CAC CTA CGG AAA CCT TGT T 19 1769-1787 2

Large Subunit (LSU) rDNA

Name Primer Sequence 5'-3' Length Position on Citrus Comments Ref.
N-S1 for CGA CCC CAG GTC AGG CGG 18 3-21 3
27 for CCC GCT GAG TTT AAG CAT A 19 26-45
36 for TTT AAG CAT ATC AAT AAG CGG AGG AAA 27 36-62
N-S2 for GAG TCG GGT TGT TTG GGA 18 264-282 3
N-S3 for AGG GAA GCG GAC GGG GGC 18 416-433 3
N-S4 for TTG AAA CAC GGA CCA AGG 18 657-674 3
N-S5 for CGT GCA AAT CGT TCG TCT 18 889-906 3
N-S6 for TGG TAA GCA GAA CTG GCG 18 1138-1155 3
N-S7 for GAT GAG TAG GAG GGC GCG 18 1376-1393 2 mismatches 3
1529 for. CAT GGG TTA GTC GAT CCT AAG 21 1526-1549
N-S8 for ACG TTA GGG AGT CCG GAG 18 1643-1660 3
1715 for. AGC CGG AGG TAG GGT CCA GC 20 1729-1748
N-S9 for AAT GTA GGC AAG GGA AGT 18 1893-1910 3
N-S10 for TAA AAC AAA GCA TTG CGA 18 2146-2163 3
N-S11 for AAT CAG CGG GGA AAG AAG 18 2390-2407 3
N-S12 for GTC CTA AGA TGA GCT CAA 18 2658-2675 3
N-S13 for CCT ATC ATT GTG AAG CAG 18 2891-2908 3
N-S14 for TTA TGA CTG AAC GCC TCT 18 3110-3127 3
G268 for CTG AAC GCC TCT AAG TCA G 19 3116-3134 5
3343 for GGC CTT GCT GCC ACG ATC CAC TGA G 25 3343-3368
N-S15 for TGC CAC GAT CCA CTG AGA 18 3351-3368 3
NTS for CTG AGA TTA AGC CTT TGT 18 3362-3379 fungal spec. 5
C- S1 rev CCG CCT GAC CTG GGG TCG 18 3 - 21 4
25 rev. TAT GCT TAA AYT CAG CGG GT 20 26-45 7
ITS-4 rev TCC TCC GCT TAT TGA TAT GC 20 41-60 6
40 rev TCC TCC GCT TAT TGA TAT GC 20 41-60
C-S2 rev TCC CAA ACA ACC CGA CTC 18 264-282 4
268 rev GCA TTC CCA AAC AAC CCG AC 20 267-285 3
307 rev TTG GGC TGC ATT CCC A 16 278-293
459 rev CTT TCC CTC ACG GTA 15 352-366 1 mismatch
C-S3 rev GCC CCC GTC CGC TTC CCT 18 416-433 4
641 rev TTG GTC CGT GTT TCA AGA CG 20 653-673 3
C-S4 rev CCT TGG TCC GTG TTT CAA 18 657-674 4
C-S5 rev TGT CGA ACG ATT TGC ACG 18 889-906 4
950 rev GCT ATC CTG AGG GAA ACT TC 20 962-981 3
C-S6 rev CGC CAG TTC TGC TTA CCA 18 1138-1155 4
1229 rev ACT TCC ATG ACC ACC GTC CT 20 1239-1261 3
C-S7 rev CGC GCC CTC CTA CTC ATC 18 1376-1393 2 mismatches 4
1499 rev ACC CAT GTG CAA GTG CCG TT 20 1516-1535 3
C-S8 rev CTC CGG ACT CCC TAA CGT 18 1643-1660 4
1715 rev GCT GGA CCC TAC CTC CGG CT 20 1729-1748
1839 rev TTC ACC TTG GAG ACC TGA TG 20 1853-1872 3
C-S9 rev ACT TCC CTT GCC TAC ATT 18 1893-1910 4
2134 rev GGA CCA TCG CAA TGC TTT GT 20 2150-2168 3
C-S10 rev TCG CAA TGC TTT GTT TTA 18 2146-2163 4
C-S11 rev CTT CTT TCC CCG CTG ATT 18 2390-2407 4
2426 rev MCT ACA CCT CTC AAG TCA T 19 2444-2562 3
3700 rev AGA GTA GTG GTA TTT CA 17 2470-2487 1 mismatch 3' end
C-S12 rev TTG AGC TCA TCT TAG GAC 18 2658-2675 4
2782 rev GGT AAC TTT TCT GAC ACC TC 20 2798-2817 3
C-S13 rev CTG CTT CAC AAT GAT AGG 18 2891-2908 4
2576a rev GGT CTA AAC CCA GCT C 16 2936-2951
3058 rev TTC GCG CCA CTG GCT TTT CA 20 3074-3093 3
C-S14 rev AGA GGC GTT CAG TCA TAA 18 3110-3127 4
3323 rev ACT CYR CCA CTT ACA ATR CC 20 3323-3342
3344 rev CTGAATCTCAGTGGATCGTGGCAGCAARRC 30 3344-3373
3331 rev ATC TCA GTG GAT CGT GGC AG 20 3350-3369 3
C-S15 rev TCT CAG TGG ATC GTG GCA 18 3351-3368 4
3336 rev CTG GAT CTC AGT GGA TCG T 19 3355-3373 1 mismatch

Internal Transcribed Spacer rDNA (ITS)

Name Primer Sequence 5'-3' Length Position on Glycine Comments Ref.
18S 1631 for TTT GTA CAC ACY GCC CGT CG 20 1631-1650 2
18S 1406 for TGY ACA CAC CGC CCG T 16 1633-1648
18S 1830 for AAC AAG GTT TCC GTA GGT GA 20 1769-1787 7
5.8S 32 rev GCT ACG TTC TTC ATC GAT GC 2 32-52 plant specific 7
5.8S 32 for GCA TCG ATG AAG AAC GTA GC 20 32-52 plant specific 7
5.8S 79 for GCA GAA TCC CGT GAA CCA TC 20 79-99 plant specific
5.8S 79 rev GAT GGT TCA CGG GAT TCT GC 20 79-99 plant specific
26S 25 rev TAT GCT TAA AYT CAG CGG GT 20 26-45 7
26S 268 rev GCA TTC CCA AAC AAC CCG AC 20 267-285
307 rev TTG GGC TGC ATT CCC A 16 278-293
Apo C ITS rev AGA TGA GGG GAC ATG TTC AC 20 - Apodanthes specific
Apo D ITS rev AGC TTT AGC ACC ACA ACT GG 20 - Apodanthes specific

Intergenic Spacer rDNA (IGS)

Name Primer Sequence 5'-3' Length Position on Glycine Comments Ref.
NTS-1 rev GAG ACA AGC ATA TGA CTA C 19 20-48 on SSU rDNA 5
145 rev CTA GYA TTR CTA CGG TTA TCC 21 141-161 on SSU rDNA 1, 2
26S-N-S14 for TTA TGA CTG AAC GCC TCT 18 3110-3127 on LSU rDNA 3
26S-G268 for CTG AAC GCC TCT AAG TCA G 19 3116-3134 on LSU rDNA 5
26S-3343 for GGC CTT GCT GCC ACG ATC CAC TGA G 25 3343-3368 Plant specific
26S-N-S15 for TGC CAC GAT CCA CTG AGA 18 3351-3368 on LSU rDNA 3
26S-NTS for CTG AGA TTA AGC CTT TGT 18 3362-3379 fungal specific 5
IGS 1 for GTG TCT TGC CAT GTT ATG 18 231-248 Glycine specific 8
IGS 2 rev GGT AGG TAG GCA ACA CA 17 1478-1494 Glycine specific 8
IGS 3 for GAC TAA AGC ATC ACC GGG AA 20 596-615 Glycine specific 8
IGS 4 rev CCC CAC AAT ACC AAA GGC AT 20 1295-1314 Glycine specific 8

References

  1. Nickrent, D. L. & C. R. Franchina. 1990. Phylogenetic relationships of the Santalales and relatives. J. Mol. Evol. 31: 294-301.
  2. Nickrent, D. L. & E. M. Starr. 1994. High rates of nucleotide substitution in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants. J. Mol. Evol. 39: 62-70.
  3. Kuzoff, R. K., J. A. Sweere, D. E. Soltis, P. S. Soltis & E. A. Zimmer. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15: 251-263.
  4. C. Bult and E. Zimmer, unpublished.
  5. L. Gray, unpublished
  6. White, T. J., T. Bruns, S. Lee & J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal genes for phylogenetics Chapter 38. Academic Press, San Diego, CA.
  7. Nickrent, D. L., K. P. Schuette & E. M. Starr. 1994. A molecular phylogeny of Arceuthobium based upon rDNA internal transcribed spacer sequences. Amer. J. Bot. 81: 1149-1160.
  8. Nickrent, D. L. & J. A. Patrick. 1998. The nuclear ribosomal DNA intergenic spacers of wild and cultivated soybean have low variation and cryptic subrepeats. Genome 41: 183-192.

SIUC / Plant Biology / Faculty/ Dan Nickrent
URL: http://www.plantbiology.siu.eduy/nickrent/primer.nuclear.html
Last updated: 25-Sept-07 / dln