PCR Primers for SSU rDNA
| Primer |
Other Names |
5' end |
3' end |
Primer Sequence |
Notes |
Reference |
| nu-SSU-0021-5' |
|
0004 |
0021 |
CTGGT TGAT TCTGC CAGT |
|
Gargas & DePriest, 1996 |
| nu-SSU-0038-5' |
NS1 |
0020 |
0038 |
GTAGT CATAT GCTTG TCTC |
|
White et al., 1990 |
| nu-SSU-0072-5' |
NS17UCB |
0054 |
0072 |
CATGT CTAAG TTTAA GCAA |
NGA |
Gargas & Taylor, 1992 |
| nu-SSU-0305-3' |
CNS26 |
0323 |
0305 |
TCGAA AGTTG ATAGG GCAG |
|
Gargas et al., 1995b |
| nu-SSU-0402-5' |
NS19UCB |
0381 |
0402 |
CCGGA GAAGG AGCCT GAGAA AC |
SIP 323, NGA |
Gargas & Taylor, 1992 |
| nu-SSU-0497-3' |
NS18UCB |
0516 |
0497 |
CTCAT TCCAA TTACA AGACC |
NGA |
Gargas & Taylor, 1992 |
| nu-SSU-0573-5' |
NS3 |
0553 |
0573 |
GCAAG TCTGG TGCCA GCAGC C |
SIP 516 |
White et al., 1990 |
| nu-SSU-0553-3' |
NS2 |
0573 |
0553 |
GGCTG CTGGC ACCAG ACTTG C |
SIP 516 |
White et al., 1990 |
| nu-SSU-0819-5' |
NS21UCB |
0802 |
0819 |
GAATA ATAGA ATAGG ACG |
NGA |
Gargas & Taylor, 1992 |
| nu-SSU-0852-3' |
NS20UCB |
0871 |
0852 |
CGTCC CTATT AATCA TTACG |
NGA |
Gargas & Taylor, 1992 |
| nu-SSU-1150-5' |
NS5 |
1128 |
1150 |
AACTT AAAGG AATTG ACGGA AG |
|
White et al., 1990 |
| nu-SSU-1131-3' |
NS4 |
1150 |
1131 |
CTTCC GTCAA TTCCT TTAAG |
|
White et al., 1990 |
| nu-SSU-1203-5' |
NS23UCB |
1184 |
1203 |
GACTC AACAC GGGGA AACTC |
NGA |
Gargas & Taylor, 1992 |
| nu-SSU-1184-3' |
MB2 |
1203 |
1184 |
GAGTT TCCCC GTGTT GAGTC |
|
Gargas et al., 1995b |
| nu-SSU-1258-5' |
SR12R |
1241 |
1258 |
GCTCT TTCTT GATTT TGT |
|
DePriest, 1993 |
| nu-SSU-1293-3' |
NS22UCB |
1312 |
1293 |
AATTA AGCAG ACAAA TCACT |
NGA |
Gargas & Taylor, 1992 |
| nu-SSU-1427-5' |
SR14R |
1410 |
1427 |
TTTGA GGCAA TAACA GGT |
|
DePriest, 1993 |
| nu-SSU-1431-5'-19 |
NS7R |
1413 |
1431 |
GAGGC AATAA CAGGT CTGT |
SIP 1199 |
White et al., 1990 |
| nu-SSU-1436-5'-24 |
NS7 |
1413 |
1436 |
GAGGC AATAA CAGGT CTGTG ATGC |
SIP 1199 |
White et al., 1990 |
| nu-SSU-1412-3' |
NS6 |
1436 |
1412 |
GCATC ACAGA CCTGT TATTG CCTC |
SIP 1199 |
White et al., 1990 |
| nu-SSU-1428-3' |
SR15 |
1445 |
1428 |
CATCT AAGGG CATCA CAG |
SIP 1210 |
DePriest, 1993 |
| nu-SSU-1465-3' |
SR16 |
1482 |
1465 |
TTGTC TCTGT CAGTG TAG |
|
DePriest, 1993 |
| nu-SSU-1583-5' |
SR18R |
1566 |
1583 |
CAACG AGGAA TTCCT AGT |
|
DePriest, 1993 |
| nu-SSU-1580-3' |
SR17 |
1597 |
1580 |
GATGA CTCGC GCTTA CTA |
|
DePriest, 1992 |
| nu-SSU-1626-5' |
SR11R |
1609 |
1626 |
ATTAC GTCCC TGCCC TTT |
SIP 1389 |
DePriest, 1992 |
| nu-SSU-1627-3' |
BMB C |
1641 |
1627 |
ACGGG CGGTG TGTRC |
|
Lane, et al., 1985 |
| nu-SSU-1766-5' |
ITS5 |
1744 |
1766 |
GGAAG TAAAA GTCGT AACAA GG |
|
White et al., 1990 |
| nu-SSU-1722-3' |
|
1747 |
1722 |
TCCTC TAAAT GACCA AGTTT GWCCA A |
|
Gargas & DePriest, 1996 |
| nu-SSU-1776-5' |
|
1750 |
1776 |
TAAAA GTCGT AACAA GGTTT CCGTA GG |
SIPs 1506, 1512 |
Gargas & DePriest, 1996 |
| nu-SSU-1750-3' |
NS24UCB |
1769 |
1750 |
AAACC TTGTT ACGAC TTTTA |
SIP 1506, NGA |
Gargas & Taylor, 1992 |
| nu-SSU-1787-5' |
ITS1 |
1769 |
1787 |
TCCGT AGGTG AACCT GCGG |
SIPs 1512, 1516 |
White et al., 1990 |
| nu-SSU-1769-3' |
NS8 |
1788 |
1769 |
TCCGC AGGTT CACCT ACGGA |
SIPs 1512, 1516 |
White et al., 1990 |
| nu-SSU-1780-3' |
PD9rev, SR13 |
1797 |
1780 |
AATGA TCCTT CCGCA GGT |
|
DePriest, 1993 |
Intron-specific Primers for SSU rDNA Introns
| Primer |
5' end |
3' end |
Primer Sequence |
Notes |
Reference |
| nu-SSI(1046)-154-5'-Ccg |
128 |
154 |
GGYCT CAGTT CGAGA TATAG TCGAG CC |
within introns at postion 1046 |
Gargas & DePriest, 1996 |
| nu-SSI(1046)-164-3'-Ccg |
184 |
164 |
TCAGC CCATC ACTCG CCTAG TCTGT GA |
within introns at postion 1046 |
Gargas & DePriest, 1996 |
| nu-SSI(1516)-194-5'-Ccg |
168 |
194 |
CACTT CGGTG GTTGA GATAT GATCG GC |
within introns at postion 1516 |
Gargas & DePriest, 1996 |
| nu-SSI(1516)-146-3'-Ccg |
172 |
146 |
AAGTG GCCGC TATCG TTTGA CCTGT GA |
within introns at postion 1516 |
Gargas & DePriest, 1996 |
Adapted from Gargas, A. & DePriest, P.T., 1996. Mycologia 88: 745-748.
download PDF (1.4 Mb).
yellow background color denotes 5' primers ("forward"),
green background color denotes 3' primers ("reverse") compared to the coding sequence.
NGA= non-green alga, i.e. designed to not match Chlamydomonas sequence.
SIP= Spans Intron Position, intron position numbers are relative to location within Escherichia coli (Gargas et al., 1995b).