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  

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