Leiden Muscular Dystrophy data pages©

PCR of DMD gene exons

(last modified September 9, 2005)

Contents

This page contains an older list of primer sequences that can be used to PCR all exons of the DMD gene. The new list, including M13-tails facilitating direct sequencing, can be found at "PCR and sequence analysis of DMD gene exons".

Table of primer sequences

Legend:
Amplified exon: the number of the exon amplified (exon numbering). Reference: (literature) reference for primer sequences. Length: length amplified fragment (usually including intronic sequences). Forward primer / Reverse primer: sequence of the respective primers with exonic sequences given in upper case, intronic and gene flanking sequences in lower case and added primer tails in italics. Name: name given to the primer (from Reference). Multiplex: indicates combined primer sets used to co-amplify the seqeunces with the Ch= Chamberlain-set, Be=Beggs-set, Ku=Kunkel-set, Ab5'=Abbs 5'-set or Ab3'=Abbs 3'-set. Letters indicate the order of the PCR-products after gel electrophoresis ('a' above 'b' etc.). DD1-, DD2- and DD3- are multiplex sets under development in our laboratory.

Amplified exon Reference Length Forward primer Reverse primer Name Multiplex Reference Length Forward primer Reverse primer Name Multiplex Reference Length Forward primer Reverse primer Name Multiplex
Dp427c promoter/exon 1 Kunkel, Boyce 332 TCTGGCTCATGTGTTTGCTCCGAGGTATAG CTTCCATGCCAGCTGTTTTTCCTGTCACTC Pb-F/R Ku-b
Dp427m promoter/exon 1 Beggs, Abbs 535 GAAGATCtagacagtggatacataacaaatgcatg ttctccgaaggtaattgcctcccagatctgagtcc PmF/R Be-a, Ab5'-a (Leiden unp.)   tagtgagcttgtcacaaac       Bushby 566 ggcaaagaatgatttacat tctgtaactttcatgtgaa PNKX/PNKW -
Dp427p promoter/exon 1 Gorecki 104 AGCaAAAAGCTTTCCTATGAAGGTG tcaggagattgagcctcgagggaga SQ/T3-R
exon X Roberts 90 GACACCATTGGAGAAATTGGTC ATGGCTCTATAAGTCAACTTTG EX5/EX3
exon 2 (Leiden unp.) 233 cactaacacatcataatgg gatacacaggtacatagtc ex2-F/R
exon 3 Beggs, Abbs 410 (b) tcatccgtcatcttcggcagattaa caggcggtagagtatgccaaatgaaaatca ex3-F/R Be-b, Ab5'-c (Leiden unp.) 286 gcattggaagtgtgctttg cgaggttgctttactaagg ex3-F2/R2   (Leiden unp.)   atcatcttcggcagattaa agtatgccaaatgaaaatca ex3-F3/R3
exon 4 Chamberlain, Abbs 196 ttgtcggtctctctgctggtcagtg caaagccctcactcaaacatgaagc ex4-F/R Ch-i, Ab5'-g SK 203 agtagattgtcggtctctctg ccaaagccctcactcaaac ex4-F2/R2
exon 5 (Leiden unp.) 225 caactaggcatttggtctc ttgtttcacacgtcaaggg ex5-F/R
exon 6 Beggs, Abbs 202 ccacatgtagGTCAAAAATGTAATGAA gtctcagtaatcttcttacCTATGACTATGG ex6-F/R Be-f, Ab5'-f (Leiden unp.) 442 gaatagactcctagccttg aacggatctggaaccatac ex6-F2/R2
exon 7 (Leiden unp.) 279 gcatggaagtaaatctcatggaac gtgtagaaatgacaagtctcagatg ex7-F/R   (Leiden unp.) 261 ctatgggcattggttgtc taaaagcagtggtagtccag ex7-F2/R2
intron 7 McNaughton, in press   extensive list (copy at this site)                
exon 8 Chamberlain, Abbs 360 ggcctcattctcatgttctaattag gtcctttacacactttacCTGTTGAG ex8-F/R Ch-f, Ab5'-d (Leiden unp.) 307 tcgtcttcctttaactttg tcttgaatagtagctgtcc ex8-F2/R2
exon 9 (Leiden unp.) 244 (c) cttctctgcagatcacg cgaggagataaaaggcac ex9-F2/R2   (Leiden unp.) 278 (a) tctatccactcccccaaacc aacaaaccagctcttcac ex9-F/R  
exon 10 Malhotra 189 gcagCATTTGGAAGC TGAGTATGAAACTGG ex10-F/R
exon 11 (Leiden unp.) 303 caaaataaaactcaaaaaccacacc cttccaaaacttgttagtcttc ex11-F2/R DD3-
exon 12 Chamberlain 331 gatagtgggctttacttacatccttc gaaagcacgcaacataagatacacct ex12-F/R Ch-g (Leiden unp.)   ctttcaaagaggtcataatagg catctgtgttactgtgtatagg ex12-F2/R2
exon 13 Beggs, Abbs 238 aataggagtacctgagatgtagcagaaat ctgacCTTAAGTTGTTCTTCCAAAGCAG ex13-F/R Be-e, Ab5'-e (Leiden unp.)   gcaaatcatttcaacacac tctttaaatcacagcacttc ex13-F2/R2   Hagiwara     aaatcacagcacttcagctg ex13-R3
exon 14 (Bartolo unp.) 431 tttgctgatgcttgattgtc caatagcataggagagactaa ex14+15-F/R
exon 15 (Bartolo unp.) 431 tttgctgatgcttgattgtc caatagcataggagagactaa ex14+15-F/R
exon 16 Kunkel 290 tctatgcaaatgagcaaatacacgc ggtatcactaacCTGTGCTGTACTC ex16-F/R Ku-c Prior 313 gcaaatgagcaaatacacg ctctgagatagtctgtagcatgat ex16-F2/R2
exon 17 Chamberlain 416 gactttcgatgttgagattactttccc aagcttgagatgctctcacCTTTTCC ex17-F/R Ch-d (Leiden unp.)   gtgctattttgatctgaagg aagcttgagatgctctca ex17-F2/R2
exon 18 (Leiden unp.) 255 ggagtctcagattgagaaaagaatg caagcagcacaaaatgagtacag ex25-F/R
exon 19 Chamberlain, Abbs 459 gatggcaaaagtgttgagaaaaagtc ttctaccacatcccattttcttcca ex19-F/R Ch-c, Ab5'-b (Leiden unp.)   gcttgaaagggcaagtag taccacatcccattttcttcc ex19-F2/R2
exon 20 (Leiden unp.) 357 tggctttcagatcatttctttc aaatacctattgattatgctcc ex20-F/R DD1-
exon 21 (Leiden unp.) 319 gcaaaatgtaatgtatgcaaag atgttagtaccttctggatttc ex21-F/R DD1-
exon 22 (Leiden unp.) 186 TTGACACTTTGCCACCAATG gataagcgtgctttattgttttgac ex22-F/R
exon 23 (Leiden unp.) 423 (b) gttttaactgatagaagatcatc
(high homology to chromosome 12 sequence - 21/23)		 tttacagtttacagtgtatcgttag ex23-F/R DD1-
exon 24 DB: Tuffery 291 ttgggcctgtgtttagacata aaatccaccccagctgtaaaa ex24-F/R
exon 25 Bebchuck 258 tgtggcagtaatttttttcag aggaaatcttagttaagtacg ex25-F/R
exon 26 (Leiden unp.) 299 atgtttcatcactgtcaataacg ttcaagcattgttgcatttctttc ex26-F/R
exon 27 DB: Tuffery 238 AGAGCTAAAGAAGAGGCCCA taactatgaccatgtattgacat ex27-F/R
exon 28 DB: Tuffery 275 gaagttttaataatgaaatggcaaaa gtacctcttttaatactgcatat ex28-F/R
exon 29 (Leiden unp.) 242 ccaatgtatttagaaaaaaaaggag gcaaattagattaaagagattttcac ex29-F/R DD3- (Leiden unp.) 293 cttaatgatatgtaaatcagaag attaatgcaaattagattaaagag ex29-F2/R2
exon 30 (Leiden unp.) 261 tacagaaaagctatcaagag caaacaaaaagaatggaagc ex30-F2/R2
exon 31
exon 32 Kunkel 253 gaccagttattgtttgaaaggcaaa ttgccaccagaaatacatacCACACAATG ex32-F/R Ku-e
exon 33 (Bartolo unp.) 401 tagatattgaccaccgctgc ttgctaagactctaatcatac ex33-F/R
exon 34 Kunkel 171 GTAACAGAAAGAAAGCAACAGTTGGAGAA CTTTCCCCAGGCAACTTCAGAATCCAAA ex34-F/R Ku-g (Leiden unp.) 338 cagaaatataaaagttccaaataagtg catgttaatacttccttacaaaatc ex34-F2/R2 DD3-
exon 35 (Leiden unp.) 271 ccgtttcataagcattaaatc agcttctagccttttctc ex35-F/R DD1-
exon 36 (Bartolo unp.) 215 tgtctaaccaataatgccatg ctggtgtacaatttggaca ex36-F/R
exon 37 (Leiden unp.) 314 ctttctcactcttctcgctcac ttcgcaagagaccatttagcac ex37-F/R
exon 38 DB: Tuffery 238 ggtttatgtttcttataaaaagtaa atttatttccactcctagtt ex38-F/R
exon 39 DB: Tuffery 400 ggattaaagtgtgtgtttaa accacctcaaaaatgttaaa ex39-F/R
exon 40 (Leiden unp.) 340 ctgcagccagaagtgcacta ggaaatgcatccctcaaaga ex40-F/R
exon 41 Kunkel 274 gttagctaactgccctgggccctgtattg tagagtagtagttgcaaacacatacgtgg ex41-F/R Ku-d (Leiden unp.) 276 tgtggttagctaactgccct gagtagtagttgcaaacacatacg ex41-F2/R2 DD2-
exon 42 Kunkel 195 CACACTGTCCGTGAAGAAACGATGATGG CTTCAGAGACTCCTCTTGCTTAAAGAGAT ex42-F/R Ku-f Abbs 155 CACACTGTCCGTGAAGAAACGATGATG TTAGCACAGAGGTCAGGAGCATTGAG ex42-F2/R2 Ab3'-i (Leiden unp.)   CACACTGTCCGTGAAGAAAC cCTTCAGAGACTCCTCTTGC ex42-F3/R3
exon 43 Beggs, Abbs 357 gaacatgtcaaagtcactggacttcatgg atatatgtgttacctacCCTTGTCGGTCC ex43-F/R Be-c, Ab3'-d (Leiden unp.)   tgcaacaccatttgctacc atcatttctgcaagtatcaag ex43-F2/R2
exon 44 Chamberlain 268 cttgatccatatgcttttacctgca tccatcacccttcagaacctgatct ex44-F/R Ch-h Abbs 426 gttgtgtgtacatgdtaggtgtgta   ex44-F2/R Ab3'-b (Leiden unp.)   tgttacttgaaactaaactctgcaaatg acaacaacagtcaaaagtaatttccatc ex43-F3/R3
exon 45 Chamberlain 547 aaacatggaacatccttgtggggac cattcctattagatctgtcgccctac ex45-F/R Ch-a Abbs 307 ctttctttgccagtacaactgcatgtg   ex45-F2/R Ab3'-e
exon 46 Beggs 148 GCTAGAAGAACAAAAGAATATCTTGTC CTTGACTTGCTCAAGCTTTTCTTTTAG ex46-F/R Ch-j (Leiden unp.) 373 ccagtttgcattaacaaatagtttgag agggttaagaagaaataaagttgtgag ex46-F2/R2
exon 47 Beggs, Abbs 181 cgttgttgcatttgtctgtttcagTTAC gtctaacCTTTATCCACTGGAGATTTG ex47-F/R Be-g, Ab3'-h (Leiden unp.)   tgatagactaatcaatagaagcaaagac aacaaaacaaaacaacaatccacatacc ex47-F2/R2
exon 48 Chamberlain, Abbs 506 ttgaatacattggttaaatcccaacatg cctgaataaagtcttccttaccacac ex48-F/R Ch-b, Ab3'-a (Leiden unp.)   tttgcttatgccttgagaattatttacc caaatgagaaaattcagtgatattgcc ex48-F2/R2
exon 49 Beggs 439 gtgcccttatgtaccaggcagaaattg gcaatgactcgttaatagccttaagatc ex49-F/R Ku-a (Leiden unp.)     gcaatgactcgttaatagcc ex49-R2 DD3
exon 50 Beggs, Abbs 271 caccaaatggattaagatgttcatgaat tctctctcacccagtcatcacttcatag ex50-F/R Be-d, Ab3'-f
exon 51 Chamberlain, Abbs 388 gaaattggctctttagcttgtgtttc ggagagtaaagtgattggtggaaaatc ex51-F/R Ch-e, Ab3'-c
exon 52 Beggs, Abbs 113 AATGCAGGATTTGGAACAGAGGCGTCC TTCGATCCGTAATGATTGTTCTAGCCTC ex52-F/R Be-i, Ab3'-k
exon 53 Abbs 212 TTGAAAGAATTCAGAATCAGTGGGATG CTTGGTTTCTGTGATTTTCTTTTGGATTG ex53-F/R Ab3'-g (Leiden unp.)   tcctccagactagcatttac ttagcctgggtgacagtg ex53-F2/R2
exon 54 Prior 450 gtttgtcctgaaaggtgggttac ttatcgtcttgaaccctcccaag ex54-F/R   (Leiden unp.) 338 tgtattctgacctgaggattc tcatggtccatccagtttc ex54-F2/R2
exon 55 (Leiden unp.) 408 aatttagttcctccatctttctct aaatacatcaggctgtataaaagc ex55-F/R DD3- (Leiden unp.)   tgcatctgaacatttggtcc ctttttctaagacgagggtg ex55-F2/R2
exon 56 (Leiden unp.) 337 tttctttrgtaattctgc ctgaaattgggatgatttac ex56-F2/R   DB: Tuffery 317 attctgcacatattcttcttcctgc ggatgatttacgtagacatgtgag ex56-F3/R2
exon 57
exon 58 (Leiden unp.) 280 ttttgagaagaatgccacaagcc aaaatatgagagctatccagacc ex58-F2/R2 DD2- (Bartolo unp.) 250 ttttgagaagaatgccacaagcc aaaatatgagagctatccagacc ex58-F3/R3
exon 59 Beggs 251 CCTGAGGAGAGAGCCCAGA TCGAGGTGATCTTGGAGA ex59-F/R   DB: Tuffery 374 actctttctttcttccagtatgacc gtaaagaagtagaccgtacCTTGAC ex59-F2/R2
exon 60 Beggs, Abbs 139 AGGAGAAATTGCGCCTCTGAAAGAGAACG CTGCAGAAGCTTCCATCTGGTGTTCAGG ex60-F/R Be-h, Ab3'-j Lenk 231 taaatattctcatcttccaatttgc ttactgtaacaaaggacaacaatg ex60-F2/R2   (Leiden unp.) 262 gaataagcccaggtatcagttc   ex60-F3
exon 61 Lenk 163 aatgagagaacataatttctctcc aatcaagatgcaataaagttaagtg ex61-F2/R2 DD1- (Leiden unp.) 150 acataatttctctccttttcc caagatgcaataaagttaagtg ex61-F/R
exon 62 Lenk 185 taatgttgtctttcctgtttgcg atacaggttagtcacaataaatgc ex62-F/R
exon 63 Lenk 194 tactcatggtaaatgctaaagtc tagcaaagtaactttcacactgc ex63-F/R
exon 64 (Leiden unp.) 180 ttctgatggaataacaaatgct cattctaggcaaactctaggc ex64-F/R3 DD2- Lenk 151 tttctgatggaataacaaatgctc atcaagatcttcaaatactggcc ex64-F2/R2
exon 65 Lenk 347 tatgagagagtcctagctagg taagcctcctgtgacagagc ex65-F/R
exon 66 (Leiden unp.) 211 gtctagtaattgttttctgctttg ataagaacagtctgtcatttccc ex66-F2/R2 DD3- Lenk 173 tctgctttgattcttcataatagG atctagaactagggtaattagcc ex66-F3/R3   (Leiden unp.)   ggtctagtaattgttttctg gtaattagccaacattaataaaag ex66-F/R
exon 67 Lenk 286 aattgctactggaattgagttgg aagaataaatatgttacctagaagg ex67-F/R
exon 68 Lenk 352 taatcgaactgatatacacctcc actaacagcaactggcacagg ex68-F/R   (Leiden unp.) 356 gatatacacctcctttgccatcttgcc aactaacagcaactggcacaggaga ex68-F3/R3
exon 69 (Leiden unp.) 231 gaacgtggtagaaggtttattaaa ctaactctcacgtcaggctg ex69-F/R DD2- Lenk 242 tcaaattagaacgtggtagaagg gaactaactctcacgtcaggc ex69-F2/R2
exon 70 (Leiden unp.) 237 tggtcattagttttgaaatcatc catcaaacaagagtgtgttctg ex70-F/R DD2- Lenk 210 tcctaaatctgatctcaccatg atcaaacaagagtgtgttctgc ex70-F2/R2   Tinsley     tgcttttgctactactcacGTTTC FEIIr
exon 71 Lenk 125 aaagcgtgtgtctccttcacc atgtgttggtggtagcagcac ex71-F/R
exon 72 Lenk 144 gatggtatctgtgactaatcac atttcaatcaatatttgcctggc ex72-F/R
exon 73 Lenk 202 acgtcacataagttttaatgagc atgctaattcctatatcctgtgc ex73-F/R
exon 74 Lenk 248 accaaaacctttgattttattttcc tttctatgtgtgcaagtgtatgc ex74-F/R
exon 75 Lenk 344 tcttttttacttttttgatgc agtgctctctgaggtttag ex75-F/R
exon 76 (Leiden unp.) 198 gtaattctgttttcttttggatgac ctacctttcttcagacaacaaaat ex76-F/R DD2- Lenk 196 aagtaattctgttttcttttggatg cttcagacaacaaaatctgagag ex76-F3/R3   (Leiden unp.)   gtcctgagtgtgtataatattttaaa   ex76-F2
exon 77 Lenk 270 taatcatggccctttaatatctg gatactgcgtgttggcttcc ex77-F/R
exon 78 Lenk 220 ttctgatatctctgcctcttcc aatgagctgcaagtggagagg ex78-F/R
exon 79 Lenk 349 agagtgatgctatctatctgcac TGCATAGACGTGTAAAACCTGCC ex79-F/R

(a)modified, after alert from S. Tuffery, (b)modified (underlined part), after alert from Sylvie Chambert. (c)submitted new primers after an alert from Christophe Philippe (VANDOEUVRE, France), stating that some alleles will not amplify with the 9F/R primers.

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