Leiden Muscular Dystrophy pages©

Markers in and around the dystrophin gene

(last modified January 6, 2006)

This page gives an overview of the markers that have been described in and directly flanking the DMD gene, including RFLP (Restriction Fragment Length Polymorphism) and VNTR (Variable Number of Tandem Repeats, CA-repeats); for details regarding their localization, see "Sequences / markers in and around the dystrophin gene" . These markers can be used for mapping studies (linkage, association) in relation to DMD/BMD and the DMD-gene. Rarely, these markers are used these to screen carriers for deletions. 

VNTR's / (CA)n-repeats

Probe name Repeat DXS nr.
(UniSTS-link)		 GDB-
link		 Localization in DMD gene Reference Length
(in bp)		 Alleles PIC/HF Primer
name		 Forward / reverse
primer
5'DYS-III c.-140132
(TA)8(CA)10		 5' Dp427c promoter Feener (1991) 4 0.59 ttttttaggtataacttacatacaataaacc /
gtgacaataagcatatcagtggctgcc
5'DYS-I c.-132222
(TG)6(TA)10		 5' Dp427c promoter Feener (1991) 5 0.61 actgtaaatgaaattgttttctaagtgcc /
cttaacaaaatgtccttcagttctatcc
5'DYS-II / sWXD2450 -129241
(CA)15		 DXS1242 DXS1242 5' Dp427c promoter Feener (1991) 206 8 0.77 tcttgatatatagggattatttgtgtttgttatac /
attatgaaactataaggaataactcatttagc
5'DYS-IV c.-123974
(TG)5(TA)4		 Dp427c intron 1 Feener (1991) 0 0 aaacaaagtaatattgttagacatgtatcc /
gttaaggttcctcttagatcatggtgtcc
5'DYS MSB / sWXD2452 c.-8043
(AC)16_30		 intron 1c Oudet (1991) 97 6 0.25 OA34/
OA35		 atggttgatactttagagattattg /
gtgtcaagtaaaatttatttacagc
5'DYS MSA
=
5'-5n1		 c.31+15515
(AC)8_24		 DXS1243 DXS1243 intron 1m Oudet (1991) 74 10 0.57 NM72/
NM73		 atcccatcctgttctatttt /
actggcatgcattattttgt
King (1995) 198 cacgacagattatatgagtcat /
aagccttatgaatactggcat
5'-5n3 (TG)23 intron 2 King (1994), King (1995) 112 9 0.76 ttcagtttctctcggtgttcct /
tacacctgcacatgtgatgaaa
5'-5n4 (AC)24 intron 4 King (1995) 133 8 0.64 gaagggaaaatgatgaataaaact /
gtcagaactttgtcacctgtc
DMDSTR07A (TC)5TT(CT)12(CA)17 (DXS206) intron 7 DB: Leiden 226 12 0.68 ttctggttttctggtctg /
gaatcaatctctctgtcaag
DMDSTR07B (AC)18 (DXS206) intron 7 DB: Leiden 231 7 0.44 agctattatctgagaaagtc /
tgaggtgaatttattaaggg
5'-7n4 (CA)8TA(CA)19 intron 25 King (1995) 165 4 0.52 gtgaagctacaaaaatattagag /
caacaatatctcaccatacttg
STR-44 (TG)6GG(TG)15
TA(TG)2(AG)14		 DXS1238 DXS1238 intron 44 Clemens (1991) 196 12 0.86 tccaacattggaaatcacatttcaa /
tcatcacaaatagatgtttcacag
IVS44SK12 (GT)18 intron 44 Kochling (1995) 181 5 0.38 cctcagtgaatgaatagcacac /
ttggtgaacagctccagaagg
IVS44SK21 (GT)22 intron 44 Kochling (1995) 165 10 0.87 ggtttgctgaacagctccag /
gctcagtgaatgaatagcacac
AFM297yd1 (GT)13 DXS1219 DXS1219 intron 44 Dib (1996), DB: Leiden 8 0.59 ttaatgtttcanccaggtaaat /
gatcactccaaaggatagattgt
P20-CA complex
(TC)11(TG)10		 DXS269 intron 44 DB: Köchling, DB: Leiden 246 >0.80 aggggaggtacagcatttct /
cacttgtctctgccacaaca
STR-45 (.1) (CA)28 DXS1237 DXS1237 intron 45 Clemens (1991) 172 13 0.89 gaggctataattctttaactttggc /
ctctttccctctttattcatgttac
STR-45.2 (AC)15 intron 45 DB: Chamberlain
AFM217xa5 (GT)15 DXS997 DXS997 intron 48 Dib (1996) 4 0.7 tggctttattttaagaggac /
gttttcagtttcctgggt
STR-48 (GT)18 intron 48 DB: Chamberlain
STR-49 (AC)24 DXS1236 DXS1236 intron 49 Clemens (1991) 249 19 0.93 cgtttaccagctcaaaatctcaac /
catatgatacgattcgtgttttgc
STR-50
=
AFM234vg7		 complex
(CA)16		 DXS1235 DXS1235 intron 50 Clemens (1991) 241 6 0.72 aaggttcctccagtaacagatttgg /
tatgctacatagtatgtcctcagac
DXS1067 DXS1067 Dib (1996) 6 0.6 tatgtcctcagactattcagatgcc /
cctccagtaacagatttgggtg
AFM072zh3 (GT)13 DXS1036 DXS1036 intron 51 Dib (1996) 6 0.73 tgcagtttattatgtttccacg /
gccattgataagtgccagat
DMD1-2c / DMD I (GT)17 DXS1241 DXS1241 intron 59 Powell (1991) 251 5 0.51 tgtctgtcttcagttatatg /
ataacttacccaagtcatgt
J66 complex [(TA)n(TG)n]n (DXS268) intron 60  Yau et al (unpublished) ~1.1 kb 0.57  gcagctatatgtttcccaagattga /
gaggttctttggaggaatac
DI623 9225-23589_9225-23542
(GAA)9_27		 intron 62 Matsumoto (2004) 141-195 18 0.91 acctgcctagtcaaggta /
cactgccatggtgaatGatc*
STR62/63 (AC)15 intron 63 Taylor et al. (unpublished) ~190-200  0.38 ttcttcgtcgatacccccattcca /
ctctttgagtttaaagttacctga
AFM283wg9 c.9286+18221_9286+18254
(CA)16-21		 DXS1214 DXS1214 intron 63 Dib (1996) 7 0.78 tagaacccaaatgacaacca /
aagatagcaggcaacaataaga
DI671 c.9808-4883_9808-4814
(CT)17_36		 intron 67 Matsumoto (2004) 239-277 14 0.81 tcgccccttcagaagtcact /
gtccagcagatcaatcgtccagc
3'DYS MSC c.*461(CA)8
(TACA)1_2(CA)6		 DXS1234 DXS1234 exon 79 (11,550) Oudet (1990), Beggs (1990),
Matsumoto (2004)		 133 5 0.34 gaaagattgtaaactaaagtgtgc /
ggatgcaaaacaatgcgctgcctc
OR
gttgtttataaaaacccctaaaaacaaaac /
ggatgcaaaacaatgcgctgcctca
OR
TGGAACGCATTTTGGGTTGT /
AACAATGCGCTGCCTCAAAG
MP1S c.*942_*956
(AAGTA)2_3		 exon 79 Roberts (1989) 995 2 ? MP15/
MP13		 aagtcgacGGCTTACCTGCTTGGTCTAG /
atatcgatGTCAGAGGTAACAGATTTGC
MP1P c.*1033_1052
(TGAT)5_6		 DXS503 DXS503 exon 79 Abbs (1990), Roberts (1989) 69 4 0.22 MP1P5/
MP1P3		 atgATCAGAGTGAGTAATCGGTTGG /
atatcgatCTAGCAGCAGGAAGCTGAATG
MP1Q c.*1554_*1565
(TAAG)3_4		 exon 79 Abbs (1990), Roberts (1989) 63 2 0.08 MP1Q5/
MP1Q3		 GCGAGTAGTTCCACACAGGTTTG /
GTAACATTTGAATCAATTTGCC
3'-19n8 (GT)18 200 kb 3'
of exon 79		 King (1994), King (1995) 148 5 0.58 aacgacttcccccactctgt /
agccccattctgtacatcaaat
AFM184xg5 DXS992 DXS992 >200 kb 3'
of exon 79		 DB: Leiden 11 0.87 aagaatgggactccatttca /
gcttatccactgggacagaa
AFM112xf2 DXS985 DXS985 >200 kb 3'
of exon 79		 Dib (1996), DB: Leiden 5 0.61 tttccaaacttcactaaaac /
aaaatgttgttgtactggtc

Matsumoto et al. (2004) describe 11 additional polymorphic makers from 25 kb to 220 kb 3 'of the dystrophin stop codon.

Legend:
Probe name: name of probe, with link to local details (when available). Repeat: type of VNTR-repeat sequence. DXS nr. (UniSTS-link): DXS numberwith link to UniSTS database at NCBI. GenBank: DXS-number with link to the Genome DataBase (GDB). Localization in DMD gene: physical localization of marker in relation to the DMD gene (see Sequences / markers in and around the dystrophin gene). Reference: reference describing marker, "DB: ..." indicating a direct submission to these pages by the group indicated. Length (in bp): length of the allele in the Genomic Reference Sequence of the DMD-gene. Alleles: number of different alleles observed. PIC/HF: PIC-value / heterozygosity frequency. Primer name: name of the primers. Forward / reverse primer: sequence of the forward and reverse primers (5' to 3').
*C in paper, G in genome sequence.

RFLP's

Marker DXS-number
(GDB-link)		 Location Reference Lengt(in bp) PIC/HF Forward / reverse primer
pERT84-1 / MaeIII DXS142
(in GDB)		 intron 1m
(L37425)		 Roberts (1989) 254 / 128+108 0.38 cagggatgcaaaggaactggg /
cagtttgtttaacagtcactc 
pERT 87-1 / BstNI DXS164
(in GDB)		 intron 12 Roberts (1989) 418 / 250+150  0.45 ctatcatgcctttgacattccag /
ctcaataagagttggattcattc
pERT87-8 / TaqI DXS164
(in GDB)		 intron 13
(L05531)		 Roberts (1989) 145 / 74+71 0.38 gtcagttggtcagtaaaagcc /
ccaattaaaaccacagcag 
pERT87-15 / TaqI DXS164
(in GDB)		 intron 16
(L05532)		 Roberts (1989) 415 / 231+184  0.44 gactttcgatgttgagattactttccc /
aagcttgagatgctctcaccttttcc
pERT87-15 / BamHI DXS164
(in GDB)		 intron 17
(L05532)		 Roberts (1989) 216 / 166+50  0.47 tccagtaacggaaagtgc /
ataattctgaatagtcacaaaaag
pERT87-15 / XmnI DXS164
(in GDB)		 intron 17
(L05532)		 Roberts (1989) 689 /
479+210 		 0.44 acaatttccctttcattccag /
gactggagcaagggtcgcc

Legend:
Marker: name of probe (marker). DXS nr. (GDB-link): DXS number with link to UniSTS database at NCBI and the Genome DataBase (GDB). Location: physical localization of marker in relation to the DMD gene (see Sequences / markers in and around the dystrophin gene). Reference: reference describing marker, "DB: ..." indicating a direct submission to these pages by the group indicated. Length (in bp): length of the allele in the Genomic Reference Sequence of the DMD-gene; italics = data not checked. PIC/HF: PIC-value / heterozygosity frequency. Primer name: name of the primers. Forward / reverse primer: sequence of the forward and reverse primers (5' to 3').

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