Copy at the Leiden Muscular Dystrophy pages©

(link to original site is not longer available)


Tables and Diagrams to accompany McNaughton et al. (1998)

McNaughton, J.C., Cockburn, D.J., Hughes, G., Jones, W.A., Laing, N.G., Ray, P.N., Stockwell, P.A., and Petersen, G.B. (1998). Is gene deletion in eukaryotes sequence-dependent? A study of nine deletion junctions and nineteen other deletion breakpoints in intron 7 of the human dystrophin gene. Gene 222, 41-51


Deletion Breakpoints and Repetitive Sequences in Intron 7 of Human Dystrophin Gene

Deletion Breakpoints and Repetitive Sequences in Intron 7 of Human Dystrophin Gene


Intron 7: primers for deletion breakpoints

Positions are those of the 110kb DNA sequence of intron 7 - Genbank Accession No U60822 - McNaughton et al. (1997) Genomics 40, 294-304.

Name Length F Position Forward Primer R Position Reverse Primer
exon 7 127 1060 AGCAGTCAGCCACACAACGACTGG 1186 CTCTACCATACTAAAAGCAGTGG
11k 269 11429 TCCCTGCATCACTCTTGAG 11697 ATGTGATGATTACAGCAGAG
14k 297 13803 GGAAACCTGAAGATTTATAG 14100 AAGCAGAAAGGGGTGACTAGAG
14.4k 1219 13803 GGAAACCTGAAGATTTATAG 15021 GGGACTGTAGAAAATGAAAG
14.8k 2120 13803 GGAAACCTGAAGATTTATAG 15922 TAGAAGAAATCGTTGTCC
15k 2578 13803 GGAAACCTGAAGATTTATAG 16380 GTATCAAACTGAATGGGG
16k 636 16321 CCTGACCATTCCAGTTTTATAG 16956 GACACATACAACCAACCGTGG
18k 1635 17363 GTAGGTGTTATTATATTTTG 18997 GAATCTCAGAACATGAAAACAGG
19k 151 19247 GAGCTGTGTACATTGGCATTG 19397 ATTACCCGCACCATGCTTGCTG
19.2k 1178 18597 TCACTGTTAATCTGATGGAGG 19774 CTGCCTTCCACCTGAGCAT
19.6 345 19430 GCAAGCAATCCATGATGG 19774 CTGCCTTCCACCTGAGCAT
19.7 701 19430 GCAAGCAATCCATGATGG 20130 AACATGGCCTGGTTTTGAGAG
20 1114 19430 GCAAGCAATCCATGATGG 20543 TCTGGGGCTTCAAAATGGCTG
20.1k 315 20568 GGAGTTAGTGGATCATATGG 20882 ATTATCTAGAACATGACTGCG
22k 1574 21273 GTCCCAGCATTTGTTTAG 22846 GGACTCCTGTATTTAATTTG
22.1k 892 21955 GGGTTAGTTTTGCTAAACAG 22846 GGACTCCTGTATTTAATTTG
23k 175 22672 GTATTTGGCCCGTAATATGAG 22846 GGACTCCTGTATTTAATTTG
24k 232 23991 TGGATGCACATCCATCAGTTG 24222 GGAATATTTTCATAACTGGTG
25k 193 24566 GGCAAGAGTACATGGTGAAG 24758 AAAACCTAGTTACTTCACCAG
26k 1237 25456 TGTGCAGGTGGCTGAGTAG 26692 ACAGAGATTTCCCGATCCAAG
26.6k 167 26526 TTCTGCTCTTTAATGGCTGAG 26692 ACAGAGATTTCCCGATCCAAG
27k 497 27213 GTGGGTACATACTAGGGGTG 27709 CCATGTACCCACAAAAATTA
27.5k 747 27213 GTGGGTACATACTAGGGGTG 27959 TGCAAATTCAAATAACCTCTG
28k 175 28203 GATGTTGTTCTTCCACTCTG 28377 GACTTGGTGTGTATAGTATG
29k 113 29379 TCACAATGCTGTAGGTAGTTG 29491 AGGCACTCTTATGCTCTGG
30k 422 29379 TCACAATGCTGTAGGTAGTTG 29800 CAGGCACTCGCACTTTCAGAG
32k 457 32214 AGCTCTGGTCTGTTGTACTTGGCTG 32670 CCATACAAGAAGCAATCCCAGCAAG
34k 544 33800 AAGCATTTGAGAACATCAGTGG 34343 TGCCAGTTACCCAGTTCCAAAG
34.1k 458 33886 TTATTCTGCATTAATAAGTTG 34343 TGCCAGTTACCCAGTTCCAAAG
35k 2461 33800 AAGCATTTGAGAACATCAGTGG 36260 CTAGGTAGTTCTATCACTTAG
36k 447 35814 GAAGGCATGACTGTGTTTTG 36260 CTAGGTAGTTCTATCACTTAG
36.2k 697 35814 GAAGGCATGACTGTGTTTTG 36510 TAAAGGGCAAGGGTTCCAC
36.8k 1273 36240 CTAAGTGATAGAACTACCTAG 37512 GACTGGAGGACATTACAGGTG
37k 710 36803 TGTAGGAATAGATCAGATGCCAG 37512 GACTGGAGGACATTACAGGTG
37.6k 1236 36803 TGTAGGAATAGATCAGATGCCAG 38038 TACTCTTACATAGAGGTAG
37.7k 1294 36803 TGTAGGAATAGATCAGATGCCAG 38096 TCTGGTAGGTAGCAGAGCTAG
39k 157 38785 GTTGAGCCCATCCTTGAG 38941 CCACTTTTGCTATTTCAGAGG
39.2k 176 39166 GGGAATTTGTCAATGATGAG 39341 GATCATGCCAGCCTTAGAAAG
40k 1560 40005 TGTATTCCCTCTCCAAATG 41564 GAAGGTAGAGCCACAACAAAGG
41k 98 40910 CCACAGAATTTGAGGTGACAC 41007 ATAGAATTCAGTTGCACCAGGCCATCAAG
41.3k 594 40971 TGATTAGTCTTGATGGCCTGG 41564 GAAGGTAGAGCCACAACAAAGG
43k 169 42732 CATGGTGTATTGCACCTTTCTCCCAAACAG 42900 GATTCTACTGTCACAAGAACCGATG
45k 592 44989 GCAACTTACGGAATGGGAGA 45580 CTACTCATGGTCTTACTGGCCA
45.3k 529 45052 ACTGTGCCAAGAACTCCTATA 45580 CTACTCATGGTCTTACTGGCCA
45.5k 173 45475 ATTATATCATCGTAGAATTCA 45647 TGGGTGTGAAGTGCTATCT
46k 800 45475 ATTATATCATCGTAGAATTCA 46274 ACCTTGTTGTGTCACCATCC
46.6k 657 46334 GTTATATATATTTTACCATG 46990 GTAATGGTCTACCAACCTTAT
47k 352 46639 GTTATCAGTTTAGGAAGAATG 46990 GTAATGGTCTACCAACCTTAT
48k 215 47546 GTTCATTGTGTACAGCGGTAG 47760 GAGAGACTGCTTAGGAAG
50k 168 49624 AATGCCCGGAGAGTACATTTG 49791 TGTACCTCACATAATGACATG
53k 899 52493 TCAGGAACATGTGGGACCTGG 53391 CACCCAACAGTTCTCTTGAATT
54k 223 53824 GTAGATGGGGCAAGTGACAGC 54046 CCTTGTGGATCAATTTGGGAAAC
55k 837 54452 GTTGAGCCGGAATGGTGAG 55288 TAAAGGAAGATACAGAAGTGAG
55.2k 185 55104 TCCTGTGTTGGGCTGCTCTTAGTTGG 55288 TAAAGGAAGATACAGAAGTGAG
58k 556 57486 GGAAGTGATATTTAGATGGAAGTCTGGG 58041 GACTTTGGTGCACTGTTGGGAAGGCAAG
58.4k 1711 57486 GGAAGTGATATTTAGATGGAAGTCTGGG 59196 GGGGTGATTTAGCGTTATCTGGTG
59k 341 59568 GAGAATGGATAATTTATACAGG 59900 CACCTATTTTACTTATACCTACTG
59.9k 179 59889 GTAAAATAGGTGAAGGGTGG 60067 GCAGAGCCAAACTCCTAGGCAGATAGG
60k 494 59889 GTAAAATAGGTGAAGGGTGG 60382 TATCCATCCTTGAGAAAGCTAG
61k 940 60890 GGTGTCTACCTCAATTATCAG 61829 TGTCATCAGTCATTGCAGAG
61.7k 221 61609 GTATGTACCTAGGACCTAATG 61829 TGTCATCAGTCATTGCAGAG
62k 290 62577 GGCCTACACTTTTTCTTTAAGG 62866 GGGAGGAATCCGTTTTAA
64k 105 64131 TGGGAGAGTCCTGAAATTCGG 64235 GAAGCAGTGGTCTAGGGCAG
64.6k 1038 64131 TGGGAGAGTCCTGAAATTCGG 65168 GTAGGAATGATGGTTTCACAG
66k 264 66006 ACAAGTGAACAGAAGTCCAG 66269 GGTCTTCCTAGCATTGTGTG
72k 408 71771 GAGTGAATTTCACACCTCTCCTTTTG 72178 GAAGTTCCTAGCCCTTAATAAAG
73k 244 73351 GGAGTTTGAAATCTGGATG 73594 GAGTAAGTTTTAATTAACAGG
73.5k 398 73351 GGAGTTTGAAATCTGGATG 73748 ATGTACCCTAAAGCTTAAAG
79k 1832 77971 GAAGCTTAGTTTGCCTGGATG 79802 GGAATAGAGCCTACCAGTGG
79.7k 84 79679 GTCGCTCACTCTGGGAGCTG 79762 TTGGATCAGAAATCTGATTTG
80k 440 79679 GTCGCTCACTCTGGGAGCTG 80118 GTCTTCCTAGGCAATAGGAATG
80.4k 352 80260 TACTTATGGCACCATTACATT 80611 CCCCACTGTTAAAATGTAACGT
80.5 1048 80235 GGATTGGATCACATATCTATGC 81282 TGCCCAATATTTAGTCTTGAG
80.6k 1023 80260 TACTTATGGCACCATTACATT 81282 TGCCCAATATTTAGTCTTGAG
80.9k 691 80592 GTTACATTTTAACAGTGG 81282 TGCCCAATATTTAGTCTTGAG
81k 149 81134 TGCCAAGCTACCATGAATCAG 81282 TGCCCAATATTTAGTCTTGAG
82k 238 82023 GTCTGATAAGACAAGCTTTGTTG 82260 GTGAGGTCTATATTCAAATG
83.4k 410 83195 GGTGGTCTAGTCAGTTGCTTG 83604 GGTTGAAGTAAAATCAATGTG
83.5k 679 83195 GGTGGTCTAGTCAGTTGCTTG 83873 CAGACATTGGATGTGCTAATT
83.6 801 83195 GGTGGTCTAGTCAGTTGCTTG 83995 GGAAAGAGCAGTTATAAG
84k 132 84501 TAGAAAGTTAAGATTGCGTAG 84632 GGAATATATGCAATTTCTAATAGG
86k 901 85613 GGCTAAGGTGTTGTACTTGAGG 86513 GGTGCAATTCTACTTCTTGAGG
87k 532 87588 GGTTGTGGGGTGGTTGTACTG 88119 GATACCAAGGGACAGCTAT
88k 804 87588 GGTTGTGGGGTGGTTGTACTG 88391 GGATGCAACTGTAGACCAGAA
89k 1127 88280 TGCTATAGAAATAGTTGTTACCAT 89406 GGGATTGTTGGGTCATATGGTAG
89.8k 178 89698 AATGTATAAGTTGAATACATAG 89875 TTTACCCCATTATTATCTG
90k 213 90069 ATTCAACACCCATGGACCAAG 90281 ACATCTCATTGCTCTTCTTAG
91k 254 90978 TCAAAGCATCATGTGCATCTG 91231 GTGTAGGGTGATGAAGAATG
92k 1117 90978 TCAAAGCATCATGTGCATCTG 92094 ATACACATATCAAGATAAG
94.3k 492 94033 TCATGTATCTTCGTAGCAGTG 94524 GAACAGCGTCAATACAGAG
94.5k 76 94449 AAATCATATCAATATGCTAG 94524 GAACAGCGTCAATACAGAG
95k 1737 94686 TCAGCATAGTTACTTTTTG 96422 TCCTCTCTAGATTATTTCTTG
95.5k 1283 95140 GTGTATCTTATAGCATCATG 96422 TCCTCTCTAGATTATTTCTTG
96k 169 96254 GTATGTATGCGACTCTCTGTG 96422 TCCTCTCTAGATTATTTCTTG
100k 838 99667 AGGAAGCTGAGGTGCATTATG 100504 GACCCAATCCTTCACACTTAG
100.3k 1373 99667 AGGAAGCTGAGGTGCATTATG 101039 GGACGAACATCACGCATTTGTG
101k 2006 99667 AGGAAGCTGAGGTGCATTATG 101672 GAGCTTAGCCTGTTGAGG
102k 240 102656 GAAGAGGGCTTTTATGGAAG 102895 ATTGAAAATATGAGACACAG
103k 131 103249 GGATTGGCTGCATGATAAG 103379 GAGCATAACAGGGAAAAAAG
104k 190 104480 GAGCCACTGTTTTCTACTTG 104669 TGCGTTGATGAAGATGATTG
105k 1241 105222 GGCTAGTTTATGACCAGAAG 106462 TATGAGTATATAGCAGATGAG
106k 184 106279 GACTTTAACTGTCCTCTG 106462 TATGAGTATATAGCAGATGAG
107k 1088 106279 GACTTTAACTGTCCTCTG 107366 GGATTGCTGGAGGAAAACTTG
108k 520 107761 ACTGGTTGTGCCAATTAGAGG 108280 GACACATGCATGTATGTTTGG
109k 213 108664 GTGTAATAAGTTGAGCCATATG 108876 GGAGCTCTGCATTTGCAATAG
exon 8 361 110557 AGGCCTCATTCTCATGTTCTAATTAG 110917 GTCCTTTACACACTTTACCTGTTGAG

Long Range PCR primers for Amplification of Deletion Junctions

Name Location Forward Primer Location Reverse Primer
Junction 1 exon5F GGTTGATTTAGTGAATATTGGAAGTACTG intron7R @19003 ACAGAAGAATCTCAGAACATGAAAACAGG
Junction 2 intron5F GGAATGAGGCTTTCTCAGTCTTGGG intron7R @45512 TGCTGTTTTTCTGTTGTTGAATTCTACGATG
Junction 3 intron5F GGAATGAGGCTTTCTCAGTCTTGGG intron7R @41095 GGCACTTATGTGTTAAAGCAGCAAGG
Junction 4 intron7F @100853 GGTCCTAATTACAATGGTGGAAGCCAG exon10R GGTCCAGGTTTACTTCACTCTCCATCAATG
Junction 5 intron7F @73424 GTCTTGAAGCACCAGGTGGCCATTTGGGCTGAG exon12R CTTATGTTGTTGTACTTGGCGTTTTAGG
Junction 6 intron7F @107316 GGGATTATGGTCCTAGCCTCCTATTTCT exon16R CACCGGGCAAAGTTATCCAGCCATG
Junction 7 intron7F@27213 GTGGGTACATACTAGGGGTGTGTGTG exon17R GGGGAGGTGGTGGTGGAAGTTCCTCTTG
Junction 8 intron7F @20494 GGAAGAGGTGAGTAACAGATCCATCAATTCAG exon21R GTCTGCATCCAGGAACATGGGTCCTTG
Junction 9 intron7F @16318 ACGCCTGACCATTCCAGTTTTATAGGGAG exon25R ACCTGTTGGCACATGTGATCCCACTGAG
Dup Junction* intron7F @62577 GGCCTACACTTTTTCTTTAAGG intron7R @45629 TGGGTGTGAAGTGCTATCT

*Duplication junction in intron 7 associated with deletion junction 2