collagen type VI alpha 1 (COL6A1) - coding DNA reference sequence

(used for mutation description)

(last modified April 9, 2010)


This file was created to facilitate the description of sequence variants in the COL6A1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008674.1, covering COL6A1 transcript NM_001848.2.

Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                     .         .         .         .                g.5042
                   gctctcactctggctgggagcagaaggcagcctcggtctctg       c.-61

 .         .         .         .         .         .                g.5102
 ggcggcggcggcggcccactctgccctggccgcgctgtgtggtgaccgcaggccccagac       c.-1

          .         .         .         .         .         .       g.5162
 ATGAGGGCGGCCCGTGCTCTGCTGCCCCTGCTGCTGCAGGCCTGCTGGACAGCCGCGCAG       c.60
 M  R  A  A  R  A  L  L  P  L  L  L  Q  A  C  W  T  A  A  Q         p.20

          .         .         .        | 02.         .         .    g.5908
 GATGAGCCGGAGACCCCGAGGGCCGTGGCCTTCCAGG | ACTGCCCCGTGGACCTGTTCTTT    c.120
 D  E  P  E  T  P  R  A  V  A  F  Q  D |   C  P  V  D  L  F  F      p.40

          .         .         .         .         .         .       g.5968
 GTGCTGGACACCTCTGAGAGCGTGGCCCTGAGGCTGAAGCCCTACGGGGCCCTCGTGGAC       c.180
 V  L  D  T  S  E  S  V  A  L  R  L  K  P  Y  G  A  L  V  D         p.60

          .         .         .         .        | 03.         .    g.7533
 AAAGTCAAGTCCTTCACCAAGCGCTTCATCGACAACCTGAGGGACAG | GTACTACCGCTGT    c.240
 K  V  K  S  F  T  K  R  F  I  D  N  L  R  D  R  |  Y  Y  R  C      p.80

          .         .         .         .         .         .       g.7593
 GACCGAAACCTGGTGTGGAACGCAGGCGCGCTGCACTACAGTGACGAGGTGGAGATCATC       c.300
 D  R  N  L  V  W  N  A  G  A  L  H  Y  S  D  E  V  E  I  I         p.100

          .         .         .         .         .         .       g.7653
 CAAGGCCTCACGCGCATGCCTGGCGGCCGCGACGCACTCAAAAGCAGCGTGGACGCGGTC       c.360
 Q  G  L  T  R  M  P  G  G  R  D  A  L  K  S  S  V  D  A  V         p.120

          .         .         .         .         .         .       g.7713
 AAGTACTTTGGGAAGGGCACCTACACCGACTGCGCTATCAAGAAGGGGCTGGAGCAGCTC       c.420
 K  Y  F  G  K  G  T  Y  T  D  C  A  I  K  K  G  L  E  Q  L         p.140

          | 04         .         .         .         .         .    g.9829
 CTCGTGGG | GGGCTCCCACCTGAAGGAGAATAAGTACCTGATTGTGGTGACCGACGGGCAC    c.480
 L  V  G  |  G  S  H  L  K  E  N  K  Y  L  I  V  V  T  D  G  H      p.160

          .         .         .         .         .         .       g.9889
 CCCCTGGAGGGCTACAAGGAACCCTGTGGGGGGCTGGAGGATGCTGTGAACGAGGCCAAG       c.540
 P  L  E  G  Y  K  E  P  C  G  G  L  E  D  A  V  N  E  A  K         p.180

          .         .         .         .         | 05         .    g.10207
 CACCTGGGCGTCAAAGTCTTCTCGGTGGCCATCACACCCGACCACCTG | GAGCCGCGTCTG    c.600
 H  L  G  V  K  V  F  S  V  A  I  T  P  D  H  L   | E  P  R  L      p.200

          .         .         .         .         .         .       g.10267
 AGCATCATCGCCACGGACCACACGTACCGGCGCAACTTCACGGCGGCTGACTGGGGCCAG       c.660
 S  I  I  A  T  D  H  T  Y  R  R  N  F  T  A  A  D  W  G  Q         p.220

          .         .         .         .         .        | 06.    g.10409
 AGCCGCGACGCAGAGGAGGCCATCAGCCAGACCATCGACACCATCGTGGACATGATC | AAA    c.720
 S  R  D  A  E  E  A  I  S  Q  T  I  D  T  I  V  D  M  I   | K      p.240

          .         | 07         .          | 08        .         . g.10882
 AATAACGTGGAGCAAGTG | TGCTGCTCCTTCGAATGCCAG | CCTGCAAGAGGACCTCCGGGG c.780
 N  N  V  E  Q  V   | C  C  S  F  E  C  Q   | P  A  R  G  P  P  G   p.260

          .         .     | 09   .         .         .         .    g.12371
 CTCCGGGGCGACCCCGGCTTTGAG | GGAGAACGAGGCAAGCCGGGGCTCCCAGGAGAGAAG    c.840
 L  R  G  D  P  G  F  E   | G  E  R  G  K  P  G  L  P  G  E  K      p.280

          .         | 10         .         .         .         .    g.12901
 GGAGAAGCCGGAGATCCT | GGAAGACCCGGGGACCTCGGACCTGTTGGGTACCAGGGAATG    c.900
 G  E  A  G  D  P   | G  R  P  G  D  L  G  P  V  G  Y  Q  G  M      p.300

     | 11    .         .         . | 12       .         .        | 13. g.13632
 AAG | GGAGAAAAAGGGAGCCGTGGGGAGAAG | GGCTCCAGGGGACCCAAGGGCTACAAG | GGA c.960
 K   | G  E  K  G  S  R  G  E  K   | G  S  R  G  P  K  G  Y  K   | G   p.320

          .         .         .         .   | 14     .         .    g.14042
 GAGAAGGGCAAGCGTGGCATCGACGGGGTGGACGGCGTGAAG | GGGGAGATGGGGTACCCA    c.1020
 E  K  G  K  R  G  I  D  G  V  D  G  V  K   | G  E  M  G  Y  P      p.340

          .         .         .       | 15 .         .         .    g.14254
 GGCCTGCCAGGCTGCAAGGGCTCGCCCGGGTTTGAC | GGCATTCAAGGACCCCCTGGCCCC    c.1080
 G  L  P  G  C  K  G  S  P  G  F  D   | G  I  Q  G  P  P  G  P      p.360

          .         .         .          | 16        .         .    g.15282
 AAGGGAGACCCCGGTGCCTTTGGACTGAAAGGAGAAAAG | GGCGAGCCTGGAGCTGACGGG    c.1140
 K  G  D  P  G  A  F  G  L  K  G  E  K   | G  E  P  G  A  D  G      p.380

          .         .         .         .   | 17     .         .    g.15433
 GAGGCGGGGAGACCAGGGAGCTCGGGACCATCTGGAGACGAG | GGCCAGCCGGGAGAGCCT    c.1200
 E  A  G  R  P  G  S  S  G  P  S  G  D  E   | G  Q  P  G  E  P      p.400

          .         .         .       | 18 .         .         .    g.15638
 GGGCCCCCCGGAGAGAAAGGAGAGGCGGGCGACGAG | GGGAACCCAGGACCTGACGGTGCC    c.1260
 G  P  P  G  E  K  G  E  A  G  D  E   | G  N  P  G  P  D  G  A      p.420

          .   | 19     .         .         .         .         .    g.16047
 CCCGGGGAGCGG | GGTGGCCCTGGAGAGAGAGGACCACGGGGGACCCCAGGCACGCGGGGA    c.1320
 P  G  E  R   | G  G  P  G  E  R  G  P  R  G  T  P  G  T  R  G      p.440

          .      | 20  .         .         .         .         .    g.17463
 CCAAGAGGAGACCCT | GGTGAAGCTGGCCCGCAGGGTGATCAGGGAAGAGAAGGCCCCGTT    c.1380
 P  R  G  D  P   | G  E  A  G  P  Q  G  D  Q  G  R  E  G  P  V      p.460

          .         | 21         .         .         .         .    g.20714
 GGTGTCCCTGGAGACCCG | GGCGAGGCTGGCCCTATCGGACCTAAAGGCTACCGAGGCGAT    c.1440
 G  V  P  G  D  P   | G  E  A  G  P  I  G  P  K  G  Y  R  G  D      p.480

          .         .  | 22      .         .         .         .    g.20990
 GAGGGTCCCCCAGGGTCCGAG | GGTGCCAGAGGAGCCCCAGGACCTGCCGGACCCCCTGGA    c.1500
 E  G  P  P  G  S  E   | G  A  R  G  A  P  G  P  A  G  P  P  G      p.500

          .         .     | 23   .         .         .         .    g.21408
 GACCCGGGGCTGATGGGTGAAAGG | GGAGAAGACGGCCCCGCTGGAAATGGCACCGAGGGC    c.1560
 D  P  G  L  M  G  E  R   | G  E  D  G  P  A  G  N  G  T  E  G      p.520

          .      | 24  .         .         .         .  | 25      . g.22157
 TTCCCCGGCTTCCCC | GGGTATCCGGGCAACAGGGGCGCTCCCGGGATAAAC | GGCACGAAG c.1620
 F  P  G  F  P   | G  Y  P  G  N  R  G  A  P  G  I  N   | G  T  K   p.540

          .         .         .         .         .     | 26   .    g.22410
 GGCTACCCCGGCCTCAAGGGGGACGAGGGAGAAGCCGGGGACCCCGGAGACGAT | AACAAC    c.1680
 G  Y  P  G  L  K  G  D  E  G  E  A  G  D  P  G  D  D   | N  N      p.560

          .         .         .         .         .         .       g.22470
 GACATTGCACCCCGAGGAGTCAAAGGAGCAAAGGGGTACCGGGGTCCCGAGGGCCCCCAG       c.1740
 D  I  A  P  R  G  V  K  G  A  K  G  Y  R  G  P  E  G  P  Q         p.580

  | 27       .         .         .       | 28 .         .         . g.23606
  | GGACCCCCAGGACACCAAGGACCGCCTGGGCCGGAC | GAATGCGAGATTTTGGACATCATC c.1800
  | G  P  P  G  H  Q  G  P  P  G  P  D   | E  C  E  I  L  D  I  I   p.600

          .    | 29    .   | 30     .         .         .         . g.24542
 ATGAAAATGTGCT | CTTGCTGTG | AATGCAAGTGCGGCCCCATCGACCTCCTGTTCGTGCTG c.1860
 M  K  M  C  S |   C  C  E |   C  K  C  G  P  I  D  L  L  F  V  L   p.620

          .         .         .         .         .         .       g.24602
 GACAGCTCAGAGAGCATTGGCCTGCAGAACTTCGAGATTGCCAAGGACTTCGTCGTCAAG       c.1920
 D  S  S  E  S  I  G  L  Q  N  F  E  I  A  K  D  F  V  V  K         p.640

          .         .         .       | 31 .         .         .    g.25236
 GTCATCGACCGGCTGAGCCGGGACGAGCTGGTCAAG | TTCGAGCCAGGGCAGTCGTACGCG    c.1980
 V  I  D  R  L  S  R  D  E  L  V  K   | F  E  P  G  Q  S  Y  A      p.660

          .         .         .         .         .         .       g.25296
 GGTGTGGTGCAGTACAGCCACAGCCAGATGCAGGAGCACGTGAGCCTGCGCAGCCCCAGC       c.2040
 G  V  V  Q  Y  S  H  S  Q  M  Q  E  H  V  S  L  R  S  P  S         p.680

          .         .       | 32 .         .         .         .    g.25503
 ATCCGGAACGTGCAGGAGCTCAAGGA | AGCCATCAAGAGCCTGCAGTGGATGGCGGGCGGC    c.2100
 I  R  N  V  Q  E  L  K  E  |  A  I  K  S  L  Q  W  M  A  G  G      p.700

          .         .         .         .         .         .       g.25563
 ACCTTCACGGGGGAGGCCCTGCAGTACACGCGGGACCAGCTGCTGCCGCCCAGCCCGAAC       c.2160
 T  F  T  G  E  A  L  Q  Y  T  R  D  Q  L  L  P  P  S  P  N         p.720

          .         .         .         .         .         .       g.25623
 AACCGCATCGCCCTGGTCATCACTGACGGGCGCTCAGACACTCAGAGGGACACCACACCG       c.2220
 N  R  I  A  L  V  I  T  D  G  R  S  D  T  Q  R  D  T  T  P         p.740

          .         .         . | 33       .         .         .    g.25808
 CTCAACGTGCTCTGCAGCCCCGGCATCCAG | GTGGTCTCCGTGGGCATCAAAGACGTGTTT    c.2280
 L  N  V  L  C  S  P  G  I  Q   | V  V  S  V  G  I  K  D  V  F      p.760

          .         .         .         .         .         .       g.25868
 GACTTCATCCCAGGCTCAGACCAGCTCAATGTCATTTCTTGCCAAGGCCTGGCACCATCC       c.2340
 D  F  I  P  G  S  D  Q  L  N  V  I  S  C  Q  G  L  A  P  S         p.780

          .         .         .         .         .         .       g.25928
 CAGGGCCGGCCCGGCCTCTCGCTGGTCAAGGAGAACTATGCAGAGCTGCTGGAGGATGCC       c.2400
 Q  G  R  P  G  L  S  L  V  K  E  N  Y  A  E  L  L  E  D  A         p.800

          .         .         .     | 34   .         .         .    g.26397
 TTCCTGAAGAATGTCACCGCCCAGATCTGCATAG | ACAAGAAGTGTCCAGATTACACCTGC    c.2460
 F  L  K  N  V  T  A  Q  I  C  I  D |   K  K  C  P  D  Y  T  C      p.820

      | 35   .         .         .         .         .         .    g.26698
 CCCA | TCACGTTCTCCTCCCCGGCTGACATCACCATCCTGCTGGACGGCTCCGCCAGCGTG    c.2520
 P  I |   T  F  S  S  P  A  D  I  T  I  L  L  D  G  S  A  S  V      p.840

          .         .         .         .         .         .       g.26758
 GGCAGCCACAACTTTGACACCACCAAGCGCTTCGCCAAGCGCCTGGCCGAGCGCTTCCTC       c.2580
 G  S  H  N  F  D  T  T  K  R  F  A  K  R  L  A  E  R  F  L         p.860

          .         .         .         .         .         .       g.26818
 ACAGCGGGCAGGACGGACCCCGCCCACGACGTGCGGGTGGCGGTGGTGCAGTACAGCGGC       c.2640
 T  A  G  R  T  D  P  A  H  D  V  R  V  A  V  V  Q  Y  S  G         p.880

          .         .         .         .         .         .       g.26878
 ACGGGCCAGCAGCGCCCAGAGCGGGCGTCGCTGCAGTTCCTGCAGAACTACACGGCCCTG       c.2700
 T  G  Q  Q  R  P  E  R  A  S  L  Q  F  L  Q  N  Y  T  A  L         p.900

          .         .         .         .         .         .       g.26938
 GCCAGTGCCGTCGATGCCATGGACTTTATCAACGACGCCACCGACGTCAACGATGCCCTG       c.2760
 A  S  A  V  D  A  M  D  F  I  N  D  A  T  D  V  N  D  A  L         p.920

          .         .         .         .         .         .       g.26998
 GGCTATGTGACCCGCTTCTACCGCGAGGCCTCGTCCGGCGCTGCCAAGAAGAGGCTGCTG       c.2820
 G  Y  V  T  R  F  Y  R  E  A  S  S  G  A  A  K  K  R  L  L         p.940

          .         .         .         .         .         .       g.27058
 CTCTTCTCAGATGGCAACTCGCAGGGCGCCACGCCCGCTGCCATCGAGAAGGCCGTGCAG       c.2880
 L  F  S  D  G  N  S  Q  G  A  T  P  A  A  I  E  K  A  V  Q         p.960

          .         .         .         .         .         .       g.27118
 GAAGCCCAGCGGGCAGGCATCGAGATCTTCGTGGTGGTCGTGGGCCGCCAGGTGAATGAG       c.2940
 E  A  Q  R  A  G  I  E  I  F  V  V  V  V  G  R  Q  V  N  E         p.980

          .         .         .         .         .         .       g.27178
 CCCCACATCCGCGTCCTGGTCACCGGCAAGACGGCCGAGTACGACGTGGCCTACGGCGAG       c.3000
 P  H  I  R  V  L  V  T  G  K  T  A  E  Y  D  V  A  Y  G  E         p.1000

          .         .         .         .         .         .       g.27238
 AGCCACCTGTTCCGTGTCCCCAGCTACCAGGCCCTGCTCCGCGGTGTCTTCCACCAGACA       c.3060
 S  H  L  F  R  V  P  S  Y  Q  A  L  L  R  G  V  F  H  Q  T         p.1020

          .         .                                               g.27265
 GTCTCCAGGAAGGTGGCGCTGGGCTAG                                        c.3087
 V  S  R  K  V  A  L  G  X                                          p.1028

          .         .         .         .         .         .       g.27325
 cccaccctgcacgccggcaccaaaccctgtcctcccacccctccccactcatcactaaac       c.*60

          .         .         .         .         .         .       g.27385
 agagtaaaatgtgatgcgaattttcccgaccaacctgattcgctagattttttttaagga       c.*120

          .         .         .         .         .         .       g.27445
 aaagcttggaaagccaggacacaacgctgctgcctgctttgtgcagggtcctccggggct       c.*180

          .         .         .         .         .         .       g.27505
 cagccctgagttggcatcacctgcgcagggccctctggggctcagccctgagctagtgtc       c.*240

          .         .         .         .         .         .       g.27565
 acctgcacagggccctctgaggctcagccctgagctggcgtcacctgtgcagggccctct       c.*300

          .         .         .         .         .         .       g.27625
 ggggctcagccctgagctggcctcacctgggttccccaccccgggctctcctgccctgcc       c.*360

          .         .         .         .         .         .       g.27685
 ctcctgcccgccctccctcctgcctgcgcagctccttccctaggcacctctgtgctgcat       c.*420

          .         .         .         .         .         .       g.27745
 cccaccagcctgagcaagacgccctctcggggcctgtgccgcactagcctccctctcctc       c.*480

          .         .         .         .         .         .       g.27805
 tgtccccatagctggtttttcccaccaatcctcacctaacagttactttacaattaaact       c.*540

          .         .         .         .         .         .       g.27865
 caaagcaagctcttctcctcagcttggggcagccattggcctctgtctcgttttgggaaa       c.*600

          .         .         .         .         .         .       g.27925
 ccaaggtcaggaggccgttgcagacataaatctcggcgactcggccccgtctcctgaggg       c.*660

          .         .         .         .         .         .       g.27985
 tcctgctggtgaccggcctggaccttggccctacagccctggaggccgctgctgaccagc       c.*720

          .         .         .         .         .         .       g.28045
 actgaccccgacctcagagagtactcgcaggggcgctggctgcactcaagaccctcgaga       c.*780

          .         .         .         .         .         .       g.28105
 ttaacggtgctaaccccgtctgctcctccctcccgcagagactggggcctggactggaca       c.*840

          .         .         .         .         .         .       g.28165
 tgagagccccttggtgccacagagggctgtgtcttactagaaacaacgcaaacctctcct       c.*900

          .         .         .         .         .         .       g.28225
 tcctcagaatagtgatgtgttcgacgttttatcaaaggccccctttctatgttcatgtta       c.*960

          .         .         .         .         .         .       g.28285
 gttttgctccttctgtgtttttttctgaaccatatccatgttgctgacttttccaaataa       c.*1020

          .                                                         g.28301
 aggttttcactcctct                                                   c.*1036

 (downstream sequence)
Legend:
Nucleotide numbering (following the rules of the HGVS for a 'Coding DNA Reference Sequence') is indicated at the right of the sequence, counting the A of the ATG translation initiating Methionine as 1. Every 10th nucleotide is indicated by a "." above the sequence. The Collagen type VI alpha 1 protein sequence is shown below the coding DNA sequence, with numbering indicated at the right starting with 1 for the translation initiating Methionine. Every 10th amino acid is shown in bold. The position of introns is indicated by a vertical line, splitting the two exons. The start of the first exon (transcription initiation site) is indicated by a '\', the end of the last exon (poly-A addition site) by a '/'. The exon number is indicated above the first nucleotide(s) of the exon. To aid the description of frame shift mutations, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.

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