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Genomic Reference Sequence of the dystrophin (DMD) gene

(last modified March 6, 2010)


Introduction

The DMD gene genomic reference sequence we currently use has been generated in collaboration with NCBI's RefSeqGene project, record NG_012232.1. This record is also used as the basis for the description of sequence variants in the DMD gene (see the DMD gene variant databases).

The reference sequence we have used in the past was constructed as described below (Table "Genomic Reference Sequence of the dystrophin (DMD) gene"). The sequence was based on the individual sequences released from the Human Genome Project (HGP), mainly completely sequenced PAC and BAC clones.

On specific issues, more detailed data can be found at;


Region DMD gene GenBank file Lentgh
(in bp)
Clone Remark
Dp527c
exon 1
AL050305
(15,033 - 14,683)
139,258 RPCI6 - 60B16 125 kb upstream - 15 kb donwstream
Dp427m
exon 1
AL031643
(20,769 - 20,495)
133,889 RPCI4 - 769D20 100 bp overlap with AL050305
123 kb upstream - 20 kb donwstream
Dp527p 
exon 1 / 
exon X
AL049643
(56,235 - 55,962)
118,695 RPCI4 - 672M15 100 bp overlap with AL031643
62 kb upstream - 56 kb donwstream
intron 1 AL139401 16,392
(>200 kb)
RPCI5 - 1154A22 100 bp overlap with AL049643 
intron 1
exon 2 AL451144 100,207 RPCI11 - 151J4 100 bp overlap with AL139401
36 kb intron 1 - 64 kb intron 2
intron 2 AL121880 87,065 RPCI5 - 1174H9 100 bp overlap with AL451144
87 kb intron 2
exon 3-9 AL096699
(not annotated)
203,006 RPCI5 - 1145L23 100 bp overlap wit AL121880
19 kb intron 2 - 32 kb intron 9
exon 10-16 AC004468 127,757 RPCI1 - 37A12 13.2 kb overlap with AL096699
34 kb intron 9 - 14 kb intron 16
exon 12-25 AC012042,
not annotated
168,223 RPCI11 - 45N17 17 kb intron 11 - 0.6 kb intron 25
intron 16 AL596023 3,996 RPCI11 - 142J18 2 kb overlap with AC004468
exon 17-29 AL031542,
not annotated
132,290 RPCI5 - 1147O16 6 kb intron 16 - 19 kb intron 29
1,977 bp overlap with AL596023
exon 30-42 AL109609 109,098 RPCI4 - 556A22 100 bp overlap with AL031542
7 kb intron 30 - exon 42]
exon 42-44 AL139278,
not annotated
95,866 RPCI4 - 639D23 [exon 42 - 2.6 kb intron 44
exon 43-44 AC096506 120,135 RPCI11 - 64I1 2,007 bp overlap with AC078957
3.5 kb intron 43 - 46 kb intron 44
intron 44 AC078957 198,088 RPCI11 - 339E16 2,007 bp overlap with AC096506
44 kb 3'exon 44 - 6 kb 5' exon 45
exon 45-50 AC093193 83,001 RPCI11 - 607K23 1,089 bp overlap with AC078957
exon 48-51 AC079864 161,874 RPCI11 - 662G16 2,646 bp overlap with AC093193
exon 52-55 AC093167 75,001 RPCI11 - 593P4 1,569 bp overlap with AC079864
exon 54-56 AC079175 163,198 RPCI11 - 122N14 2,072 bp overlap with AC093167
4 kb intron 53 - 8 kb intron 56
exon 57-61 AC079177 155,533 RPCI11 - 147B14 2,000 bp overlap with AC079175
4 kb intron 56 - 3 kb intron 61
exon 62 AC090632 34,346 RPCI11 - 674B1 2,008 bp overlap with AC079177
24 kb intron 61 - 10 kb intron 62
exon 63-77 AC078958 187,547 RPCI11 - 609C15 1,972 bp overlap with AC090632
44 kb intron 62 - 6.3 kb intron 77
exon 78
(65-79)
AC079143 5,303 RPCI11 - 346D13 2,000 bp overlap with AC078958
2.9 kb intron 62 - 2.3 kb intron 78
exon 79 AC006061 98,056 BAC GSHB-19O24 1,998 bp overlap with AC079143
4.3 kb intron 78 - 91 kb downstream
DXS1093 AC117405 153,177 RPCI11 -
340I10
1,999 overlap with AC006061

Legend:
Region DMD gene: DMD gene region covered by the respective sequence file. GenBank file: accession number of the sequence in GenBank. Lentgh (in bp): length of sequence in the GenBank file as used for the DMD genomic Reference Sequence. Clone: clone-ID. Remark: details on the clone. 



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