Supplemental Primer tables A to F: Lowe et.al. 2003, Genomics
Table A. PCR primers for RH mapping genes on CFA37
Gene name |
Target region |
Sequence 5'—3' |
Tm |
GenBank Accession no. |
AAMP |
Exon 3 |
TTTTCTGGAGGAAAGACATGG |
TD65 |
AY197355 |
|
Exon 3 |
TAAGACCTCCAGGAGAACAGG |
|
|
CRYBA2 |
Intron 4 |
GATGGGGTGCTAAGAGATAGG |
TD65 |
AY197368 |
|
Intron 4 |
CTATTCCCACCCTCCATTGC |
|
|
DES |
Intron 4 |
AACTCCGCATCTCACTACTCC |
58 |
AY197369 |
|
Intron 5 |
CATGATTCCTGAGAGTTCAGC |
|
|
EPHA4 |
Intron 2 |
TGTGAGGGTAAAGTGGAACTG |
58 |
AY197356 |
|
Exon 3 |
CTGTTGCAGTCTCTCAATGTG |
|
|
GMPPA |
Intron 4 |
CAGGCTCATGCTTTCTGC |
TD65 |
AY197357 |
|
Intron 5 |
CTCTGCATTCCAAGGTACTCC |
|
|
NLI-IF |
Exon 7 |
CAAAATGGTTGAAAGTCATGG |
TD65 |
AY197358 |
|
Exon 7 |
AAAAGTCCACGGGTGAGG |
|
|
NRP2 |
3'UTR |
GAAACGTCAGATGTGATTTGG |
58 |
AY197359 |
|
Exon 17 |
GGGCTTCTGCTCTACTGTACC |
|
|
PRKAG3 |
Intron 11 |
CCCAGTAGATCATTCTGAAAGC |
TD65 |
AY197360 |
|
Intron 12 |
ACACTGCCCACTACACATCC |
|
|
PTPRN |
Exon 13 |
CTTGTCTCGCTGCTGTGC |
60 |
AY197361 |
|
Intron 12 |
CAGCTTTGCCCTAGAGATACC |
|
|
Q9P1A4/TERP |
Exon 8 |
TTTCCTTAGCTTAGAGCTTGC |
58 |
AY197362 |
|
Exon 6 |
ATGTTTGCAGGGTACTTTGG |
|
|
RPL37A |
Exon 1 |
CAAAACACTTCTTCCTCTCTGG |
58 |
AY197363 |
|
3'UTR |
GACCGGGTCTTTTGAATAGC |
|
|
PAX3 |
Exon 6 |
AGCTGGAGCCAATCAACTGATGG |
56 |
AY197354 |
|
Intron 7 |
TCGCTCAGACCAAGCCCTCGT |
|
|
SLC4A3 |
Intron 9 |
GACCCGTTTCTACCAGACG |
58 |
AY197364 |
|
Intron 9 |
GAGGACGCAGAACTGAATAGG |
|
|
TNP1 |
Intron 1 |
TACTGGGGCAGGAAGAGG |
60 |
AY197370 |
|
3'UTR |
CATTTAACCCACACGATAGGC |
|
|
TNS |
Intron 31 |
CCCGCCTATTTCTGTAATCC |
56 |
AY197365 |
|
Intron 31 |
ACCCAACACAATTACTCATGG |
|
|
VIL1 |
Exon 13 |
TAAGGATGAAGACGTCATTGG |
56 |
AY197366 |
|
Intron 12 |
CTGGTAATGATGCGTCAGG |
|
|
XRCC5 |
Intron 2 |
GTGTTCTGTTGTTGACAGTGG |
58 |
AY197367 |
|
Exon 3 |
ATTTCATCCCTGCTCTCAGC |
|
|
Table B. Primers for amplification of AAMP from genomic DNA
Target Exon(s) |
|
Primer sequence 5'—3' |
Tm |
2 |
F- |
GAGATTATCGAGGTGGTAGAGC |
TD60/75s |
|
R- |
GTAAGGAGCAAAAGCAGATCC |
|
4-5 |
F- |
GCAGATGATCTAGTCTGTTTTGG |
58 |
|
R- |
ACAGGTAGCTGGGCAGTTG |
|
4-5 |
F- |
TTCAGCCACGACTCTACCC |
TD60/45s |
|
R- |
ACTGGGCAGAAAGGAAGG |
|
7-9 |
F- |
TATGAAGATGGCACCATCAGG |
TD62/45s |
|
R- |
AGATAGAAGGAGGGCATCAGG |
|
11 |
F- |
ATCGTGCAGCTGCTGTGG |
TD62/2min |
|
R- |
TAGCTTTGTGGTCTCCTGACG |
|
Table C. Primers for amplification of AAMP from cDNA
Target Exon(s) |
|
Primer sequence 5'—3' |
Tm |
1-5 |
F- |
GAGATTATCGAGGTGGTAGAGC |
TD60/45s |
|
R- |
ACAGGTAGCTGGGCAGTTG |
|
4-7 |
F- |
TTCAGCCACGACTCTACCC |
TD59/45s |
|
R- |
AAAGACTCCACGGAGTTGG |
|
6-10 |
F- |
TATGAAGATGGCACCATCAGG |
TD62/1min |
|
R- |
TACTTGCTGAGGGCAAAGTCC |
|
10-3'UTR |
F- |
ATCGTGCAGCTGCTGTGG |
TD62/2min |
|
R- |
CGGCCGCTCTAGAAGTACTCTCG |
|
Table D. Primers for exon scanning of AAMP
Target Exon(s) |
|
Primer sequence 5'—3' |
Tm-(1) |
1 |
F- |
GTCGCCTACGCCTACTTCC |
TD60/45s |
|
R- |
GCTTAGCGGAGAAGTGTGG |
|
2 |
F- |
AGCTCCCCACACTTCTCC |
TD60/45s |
|
R- |
AGGCGTCTGATGTTCAGC |
|
3 |
F- |
TTTTCTGGAGGAAAGACATGG |
TD60/45s |
|
R- |
TAAGACCTCCAGGAGAACAGG |
|
4 |
F- |
AGAGGACGTAAGCCTGAGC |
TD60/45s |
|
R- |
ACGGAGTAGACACCCTTGC |
|
5 |
F- |
CTCCCTGCTGACCCTTCC |
TD62/30s |
|
R- |
GGAGCCAACCTCTGTACACC |
|
6-7 |
F- |
GGTCTGCTCCCTTACTTTCC |
TD60/45s |
|
R- |
CAACAGGAGACGCACAGG |
|
8-9 |
F- |
CTGTGCGTCTCCTGTTGC |
TD60/45s |
|
R- |
CAGACTCTCAGGGACAGAGG |
|
10 |
F- |
AGGTGCCTGTCAGCTTCC |
TD60/45s |
|
R- |
CACCTCCCAATCACACAGG |
|
11 |
F- |
TCTAGAATCAAGGCTGCACTG |
TD58/30s |
|
R- |
AAGGGGTTGGAACACAGTCC |
|
1- PCR conditions are the same as those used for RH typing .for all touchdown
programs are modified as follows: 7 cycles beginning at Tm+6°C, followed
by 28 cycles at Tm. Extension times are 20 sec unless otherwise indicated.
Table E. Primers for probes used to screen the canine BAC library
Gene name |
Target region |
Sequence 5'—3' |
Tm |
TNS |
Intron 5 |
CTGGGATCACAGGTTGAAGG |
60 |
|
Exon 6 |
CCATGCTTGGACTTGAGC |
|
DES |
Intron 4 |
CAAGGCTCTGGGAACAGG |
TD65 |
|
Intron 6 |
TCATCAGGGAATCATTCTGC |
|
CRYBA2 |
Intron 2 |
AAGACCCAACTAACATTGATGC |
60 |
|
Intron 3 |
CTCTTAGCACCCCATCACC |
|
TNP1 |
5'UTR |
GGGTTTCCTAGAGTCACATCC |
60 |
|
Exon 2 |
CATTTAACCCACACGATAGGC |
|
GMPPA |
Intron 4 |
ACTGTGGTCTCTGGACTAGGG |
58 |
|
Intron 5 |
CTCTGCATTCCAAGGTACTCC |
|
XRCC5 |
Intron 3 |
ACTCTGGGGAGCCTCATC |
60 |
|
Intron 2 |
AGAGCCTAGGAATTGTCATTG |
|
PRKAG3 |
Intron 11 |
TGTGACTGTGTGATCTGTGG |
60 |
|
Intron 13 |
GTCCCCTAGAGACCAGTTAGG |
|
VIL1 |
Intron 15 |
CCCAGGAAGGATGAATAAGG |
58 |
|
Intron 13 |
CAAGATGGTTGCTGACACC |
|
EPHA4 |
Intron 2 |
GTGAGGGTAAAGTGGAACTGG |
TD65 |
|
Intron 3 |
CAGATCTGAGTGCCTGTTAGC |
|
Table F.1. Primers defining microsatellite markers on CFA37
Marker name-(a) |
Repeat |
|
Sequence 5'—3' |
Tm |
DTR37.25-(b) |
GGAA |
F- |
GCCATACTTCAGAAGCAGAA |
|
|
|
R- |
AGGCTGACACTGGAACTTTA |
|
FH1452 |
GT |
F- |
CACTGCGCCGGGTATAGG |
58 |
|
|
R- |
GAACCACAGGTAGGTCCTCTCC |
|
FH1469 |
GT |
F- |
CATCTTAGTAGATGCAGGAAAACC |
58 |
|
|
R- |
TCCAAATCAGCTTTATTGAGG |
|
FH1478 |
CA |
F- |
GGATCAAAACAGTCAGCAGC |
TD65 |
|
|
R- |
TGTATGGATGTGTGTTAGGGC |
|
FH1495 |
CA |
F- |
TTACAGGCTTAGGAGGAGG |
TD65 |
|
|
R- |
TCTCTCTCCCTCTTGACTCC |
|
FH4287 |
GAAA |
F- |
AGGCTGAGTTCACGCTCTC |
58 |
|
|
R- |
AATTTCTGTTGCTGCCATTC |
|
FH4300 |
GAAA |
F- |
TGCACAAAGCAGTCCTATTTC |
58 |
|
|
R- |
CAAGTGACAAAGGGTCCTAAG |
|
FH4306 |
CTTT |
F- |
TTCAGAGTGATGCGTGGTAG |
TD65 |
|
|
R- |
TGCACCAATGTCAAGCATAC |
|
FH4351 |
GAAA |
F- |
AAGAAGAGAAAGGCTCAGGC |
60 |
|
|
R- |
CTGCTGTCAGAAAGACCAGG |
|
FH2708 |
CA |
F- |
CAGCAATTGGACAAGAAAAAG |
60 |
|
|
R- |
GAAAGAGGATGAAGGGTGTG |
|
FH2986 |
CTTT |
F- |
ACAAGGGTTCCATCTTTTCC |
56 |
|
|
R- |
TCCTCATACCCATTAGAACAGC |
|
FH3207 |
GAAA |
F- |
AACCCTGTGTAGGCTCTGC |
60 |
|
|
R- |
GCACCCATTGCTTTGTACG |
|
FH3272 |
GAAA |
F- |
GGATCCGGGATAGAGCAG |
60 |
|
|
R- |
CTTCCCCAATCTTCCTTGTC |
|
FH3423 |
GAAA |
F- |
TCTGGAATGCCATAATTGTTC |
58 |
|
|
R- |
TGCAGGCAATGATGATTTAAG |
|
FH3449 |
CTTT |
F- |
GCAGTCCCTTCTGATCACACT |
56 |
|
|
R- |
GTGCGGGATGAGTAGAAGC |
|
FH4471 |
GA |
F- |
ACATAGTCCCTTGTTTCTGGC |
58 |
|
|
R- |
AAAAGGAATAAGCTGGTGTGC |
|
a- Markers in this table are previously unpublished except where noted.
b- GenBank Accession No. AJ279976 [5]
Table F.2. Primers for BAC end sequences on CFA37
Marker name |
|
Sequence 5'—3' |
Tm |
372-C15 |
F- |
ATTTACATGGCAGTGTGTTCTG |
58 |
|
R- |
GCCTGTACCTGACTACAACTCC |
|
374-E01 |
F- |
ACCTTGGTATGGTTTCTCACAG |
58 |
|
R- |
TTGAATTAACTTTCCCTTGTGG |
|
376-G19 |
F- |
CTGGTCACTAGGGAATTAGTGC |
58 |
|
R- |
CCTCAGATACCTGGCTCAGTAG |
|
381-P1 |
F- |
TTTGCTTGAATATAAACCCCAG |
56 |
|
R- |
GAAGCAGCAAGATTGTTGAAAG |
|
Dog
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