collagen type VI alpha 2 (COL6A2) - 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 COL6A2 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008675.1, covering COL6A2 transcript variant-1 (NM_001849.3). Transcript variants-2C2a' (NM_058175.2) and -2C2a (NM_058174.2) contain alternative 3'-terminal exons 28b and 28c (exon 28c starting in exon 28b and using the same polyA-addition site) in intron 27. 

Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                                         .         .                g.5022
                                       gcttactcggcgcccgcgcctc       c.-61

 .         .         .         .   | 02     .         .             g.18358
 gggccgtcgggagcggagcctcctcgggaccag | gacttcagggccacaggtgctgccaag    c.-1

          .         .         .         .         .         .       g.18418
 ATGCTCCAGGGCACCTGCTCCGTGCTCCTGCTCTGGGGAATCCTGGGGGCCATCCAGGCC       c.60
 M  L  Q  G  T  C  S  V  L  L  L  W  G  I  L  G  A  I  Q  A         p.20

          .         .         .         .         .      | 03  .    g.18865
 CAGCAGCAGGAGGTCATCTCGCCGGACACTACCGAGAGAAACAACAACTGCCCAG | AGAAG    c.120
 Q  Q  Q  E  V  I  S  P  D  T  T  E  R  N  N  N  C  P  E |   K      p.40

          .         .         .         .         .         .       g.18925
 ACCGACTGCCCCATCCACGTGTACTTCGTGCTGGACACCTCGGAGAGCGTCACCATGCAG       c.180
 T  D  C  P  I  H  V  Y  F  V  L  D  T  S  E  S  V  T  M  Q         p.60

          .         .         .         .         .         .       g.18985
 TCCCCCACGGACATCCTGCTCTTCCACATGAAGCAGTTCGTGCCGCAGTTCATCAGCCAG       c.240
 S  P  T  D  I  L  L  F  H  M  K  Q  F  V  P  Q  F  I  S  Q         p.80

          .         .         .         .         .         .       g.19045
 CTGCAGAACGAGTTCTACCTGGACCAGGTGGCGCTGAGCTGGCGCTACGGCGGCCTGCAC       c.300
 L  Q  N  E  F  Y  L  D  Q  V  A  L  S  W  R  Y  G  G  L  H         p.100

          .         .         .         .         .         .       g.19105
 TTCTCTGACCAGGTGGAGGTGTTCAGCCCACCGGGCAGCGACCGGGCCTCCTTCATCAAG       c.360
 F  S  D  Q  V  E  V  F  S  P  P  G  S  D  R  A  S  F  I  K         p.120

          .         .         .         .         .         .       g.19165
 AACCTGCAGGGCATCAGCTCCTTCCGCCGCGGCACCTTCACCGACTGCGCGCTGGCCAAC       c.420
 N  L  Q  G  I  S  S  F  R  R  G  T  F  T  D  C  A  L  A  N         p.140

          .         .         .         .         .         .       g.19225
 ATGACGGAGCAGATCCGGCAGGACCGCAGCAAGGGCACCGTCCACTTCGCCGTGGTCATC       c.480
 M  T  E  Q  I  R  Q  D  R  S  K  G  T  V  H  F  A  V  V  I         p.160

          .         .         .         .         .         .       g.19285
 ACCGACGGCCACGTCACCGGCAGCCCCTGCGGGGGCATCAAGCTGCAGGCCGAGCGGGCC       c.540
 T  D  G  H  V  T  G  S  P  C  G  G  I  K  L  Q  A  E  R  A         p.180

          .         .         .         .         .         .       g.19345
 CGCGAGGAGGGCATCCGGCTCTTCGCCGTGGCCCCCAACCAGAACCTGAAGGAGCAGGGC       c.600
 R  E  E  G  I  R  L  F  A  V  A  P  N  Q  N  L  K  E  Q  G         p.200

          .         .         .         .         .         .       g.19405
 CTGCGGGACATCGCCAGCACGCCGCACGAGCTCTACCGCAACGACTACGCCACCATGCTG       c.660
 L  R  D  I  A  S  T  P  H  E  L  Y  R  N  D  Y  A  T  M  L         p.220

          .         .         .         .         .     | 04   .    g.19691
 CCCGACTCCACCGAGATCGACCAGGACACCATCAACCGCATCATCAAGGTCATG | AAACAC    c.720
 P  D  S  T  E  I  D  Q  D  T  I  N  R  I  I  K  V  M   | K  H      p.240

          .      | 05  .         .         .         .         .    g.20934
 GAAGCCTACGGAGAG | TGCTACAAGGTGAGCTGCCTGGAAATCCCTGGGCCCTCTGGCCCC    c.780
 E  A  Y  G  E   | C  Y  K  V  S  C  L  E  I  P  G  P  S  G  P      p.260

          .         .  | 06      .         .         .         .    g.22792
 AAGGGCTACCGTGGACAGAAG | GGTGCCAAGGGCAACATGGGTGAGCCGGGAGAGCCTGGC    c.840
 K  G  Y  R  G  Q  K   | G  A  K  G  N  M  G  E  P  G  E  P  G      p.280

          .      | 07  .         .         .         .         .    g.22935
 CAGAAGGGAAGACAG | GGAGACCCGGGCATCGAAGGCCCCATTGGATTCCCAGGACCCAAG    c.900
 Q  K  G  R  Q   | G  D  P  G  I  E  G  P  I  G  F  P  G  P  K      p.300

  | 08       .         .        | 09.         .         .     | 10   . g.23657
  | GGCGTTCCTGGCTTCAAAGGAGAGAAG | GGTGAATTTGGAGCCGACGGTCGCAAG | GGGGCC c.960
  | G  V  P  G  F  K  G  E  K   | G  E  F  G  A  D  G  R  K   | G  A   p.320

          .         .         .          | 11        .         .    g.24302
 CCTGGCCTGGCTGGCAAGAACGGGACCGATGGACAGAAG | GGCAAGCTGGGGCGCATCGGA    c.1020
 P  G  L  A  G  K  N  G  T  D  G  Q  K   | G  K  L  G  R  I  G      p.340

          .         .         .    | 12    .         .         .    g.24782
 CCTCCTGGCTGCAAGGGAGACCCTGGAAACCGG | GGCCCCGACGGTTACCCGGGGGAAGCA    c.1080
 P  P  G  C  K  G  D  P  G  N  R   | G  P  D  G  Y  P  G  E  A      p.360

          .         .         .       | 13 .         .         .    g.25519
 GGGAGTCCAGGGGAGCGAGGAGACCAAGGCGGCAAG | GGGGACCCTGGCCGCCCAGGACGC    c.1140
 G  S  P  G  E  R  G  D  Q  G  G  K   | G  D  P  G  R  P  G  R      p.380

          .         .         .          | 14        .         .    g.25932
 AGAGGGCCCCCGGGAGAAATCGGGGCCAAGGGAAGCAAG | GGGTATCAAGGCAACAGTGGA    c.1200
 R  G  P  P  G  E  I  G  A  K  G  S  K   | G  Y  Q  G  N  S  G      p.400

          .         .         .         .         .         .       g.25992
 GCCCCAGGAAGTCCTGGTGTGAAAGGAGCCAAGGGCGGGCCTGGGCCCCGCGGACCCAAA       c.1260
 A  P  G  S  P  G  V  K  G  A  K  G  G  P  G  P  R  G  P  K         p.420

           | 15        .         .         .         .         .    g.26720
 GGCGAGCCG | GGGCGCAGGGGAGACCCCGGCACCAAGGGCAGCCCAGGCAGCGATGGCCCC    c.1320
 G  E  P   | G  R  R  G  D  P  G  T  K  G  S  P  G  S  D  G  P      p.440

          .   | 16     .         .         .         .         .    g.27444
 AAGGGGGAGAAG | GGGGACCCTGGCCCTGAGGGGCCCCGCGGCCTGGCTGGAGAGGTTGGC    c.1380
 K  G  E  K   | G  D  P  G  P  E  G  P  R  G  L  A  G  E  V  G      p.460

          .      | 17  .         .         .         .         .    g.27987
 AACAAAGGAGCCAAG | GGAGACCGAGGCTTGCCTGGACCCAGAGGCCCCCAGGGAGCTCTT    c.1440
 N  K  G  A  K   | G  D  R  G  L  P  G  P  R  G  P  Q  G  A  L      p.480

          .         | 18         .         .         .         .    g.28479
 GGGGAGCCCGGAAAGCAG | GGATCTCGGGGAGACCCCGGTGATGCAGGACCCCGTGGAGAC    c.1500
 G  E  P  G  K  Q   | G  S  R  G  D  P  G  D  A  G  P  R  G  D      p.500

          .         .  | 19      .         .         .         .    g.29028
 TCAGGACAGCCAGGCCCCAAG | GGAGACCCCGGCAGGCCTGGATTCAGCTACCCAGGACCC    c.1560
 S  G  Q  P  G  P  K   | G  D  P  G  R  P  G  F  S  Y  P  G  P      p.520

          .   | 20     .         .         .         | 21         . g.29768
 CGAGGAGCACCC | GGAGAAAAAGGCGAGCCCGGCCCACGCGGCCCCGAG | GGAGGCCGAGGC c.1620
 R  G  A  P   | G  E  K  G  E  P  G  P  R  G  P  E   | G  G  R  G   p.540

          .         .         .         .         .  | 22      .    g.31541
 GACTTTGGCTTGAAAGGAGAACCTGGGAGGAAAGGAGAGAAAGGAGAGCCT | GCGGATCCT    c.1680
 D  F  G  L  K  G  E  P  G  R  K  G  E  K  G  E  P   | A  D  P      p.560

          .         .         .         .         .     | 23   .    g.31772
 GGTCCCCCTGGTGAGCCAGGCCCTCGGGGGCCAAGAGGAGTCCCAGGACCCGAG | GGTGAG    c.1740
 G  P  P  G  E  P  G  P  R  G  P  R  G  V  P  G  P  E   | G  E      p.580

          .         .         . | 24       .         .         .    g.32177
 CCCGGCCCCCCTGGAGACCCCGGTCTCACG | GAGTGTGACGTCATGACCTACGTGAGGGAG    c.1800
 P  G  P  P  G  D  P  G  L  T   | E  C  D  V  M  T  Y  V  R  E      p.600

          .       | 25 .         .         .         .         .    g.32390
 ACCTGCGGGTGCTGCG | ACTGTGAGAAGCGCTGTGGCGCCCTGGACGTGGTCTTCGTCATC    c.1860
 T  C  G  C  C  D |   C  E  K  R  C  G  A  L  D  V  V  F  V  I      p.620

          .         .         .         .         .         .       g.32450
 GACAGCTCCGAGAGCATTGGGTACACCAACTTCACACTGGAGAAGAACTTCGTCATCAAC       c.1920
 D  S  S  E  S  I  G  Y  T  N  F  T  L  E  K  N  F  V  I  N         p.640

          .         .         .         .          | 26        .    g.32677
 GTGGTCAACAGGCTGGGTGCCATCGCTAAGGACCCCAAGTCCGAGACAG | GGACGCGTGTG    c.1980
 V  V  N  R  L  G  A  I  A  K  D  P  K  S  E  T  G |   T  R  V      p.660

          .         .         .         .         .         .       g.32737
 GGCGTGGTGCAGTACAGCCACGAGGGCACCTTTGAGGCCATCCAGCTGGACGACGAACGT       c.2040
 G  V  V  Q  Y  S  H  E  G  T  F  E  A  I  Q  L  D  D  E  R         p.680

          .         .         .         .         .         .       g.32797
 ATCGACTCCCTGTCGAGCTTCAAGGAGGCTGTCAAGAACCTCGAGTGGATTGCGGGCGGC       c.2100
 I  D  S  L  S  S  F  K  E  A  V  K  N  L  E  W  I  A  G  G         p.700

          .         .         .         .         .         .       g.32857
 ACCTGGACACCCTCAGCCCTCAAGTTTGCCTACGACCGCCTCATCAAGGAGAGCCGGCGC       c.2160
 T  W  T  P  S  A  L  K  F  A  Y  D  R  L  I  K  E  S  R  R         p.720

          .         .         .         .         .         .       g.32917
 CAGAAGACACGTGTGTTTGCGGTGGTCATCACGGACGGGCGCCACGACCCTCGGGACGAT       c.2220
 Q  K  T  R  V  F  A  V  V  I  T  D  G  R  H  D  P  R  D  D         p.740

          .         .         .         .         .         .       g.32977
 GACCTCAACTTGCGGGCGCTGTGCGACCGCGACGTCACAGTGACGGCCATCGGCATCGGG       c.2280
 D  L  N  L  R  A  L  C  D  R  D  V  T  V  T  A  I  G  I  G         p.760

          .         .         .         .         .         .       g.33037
 GACATGTTCCACGAGAAGCACGAGAGTGAAAACCTCTACTCCATCGCCTGCGACAAGCCA       c.2340
 D  M  F  H  E  K  H  E  S  E  N  L  Y  S  I  A  C  D  K  P         p.780

          .         .         .         .         .         .       g.33097
 CAGCAGGTGCGCAACATGACGCTGTTCTCCGACCTGGTCGCTGAGAAGTTCATCGATGAC       c.2400
 Q  Q  V  R  N  M  T  L  F  S  D  L  V  A  E  K  F  I  D  D         p.800

          .         .   | 27     .         .         .         .    g.33422
 ATGGAGGACGTCCTCTGCCCGG | ACCCTCAGATCGTGTGCCCAGACCTTCCCTGCCAAACA    c.2460
 M  E  D  V  L  C  P  D |   P  Q  I  V  C  P  D  L  P  C  Q  T      p.820

   | 28      .         .         .         .         .         .    g.38894
 G | AGCTGTCCGTGGCACAGTGCACGCAGCGGCCCGTGGACATCGTCTTCCTGCTGGACGGC    c.2520
 E |   L  S  V  A  Q  C  T  Q  R  P  V  D  I  V  F  L  L  D  G      p.840

          .         .         .         .         .         .       g.38954
 TCCGAGCGGCTGGGTGAGCAGAACTTCCACAAGGCCCGGCGCTTCGTGGAGCAGGTGGCG       c.2580
 S  E  R  L  G  E  Q  N  F  H  K  A  R  R  F  V  E  Q  V  A         p.860

          .         .         .         .         .         .       g.39014
 CGGCGGCTGACGCTGGCCCGGAGGGACGACGACCCTCTCAACGCACGCGTGGCGCTGCTG       c.2640
 R  R  L  T  L  A  R  R  D  D  D  P  L  N  A  R  V  A  L  L         p.880

          .         .         .         .         .         .       g.39074
 CAGTTTGGTGGCCCCGGCGAGCAGCAGGTGGCCTTCCCGCTGAGCCACAACCTCACGGCC       c.2700
 Q  F  G  G  P  G  E  Q  Q  V  A  F  P  L  S  H  N  L  T  A         p.900

          .         .         .         .         .         .       g.39134
 ATCCACGAGGCGCTGGAGACCACACAATACCTGAACTCCTTCTCGCACGTGGGCGCAGGC       c.2760
 I  H  E  A  L  E  T  T  Q  Y  L  N  S  F  S  H  V  G  A  G         p.920

          .         .         .         .         .         .       g.39194
 GTGGTGCACGCCATCAATGCCATCGTGCGCAGCCCGCGTGGCGGGGCCCGGAGGCACGCA       c.2820
 V  V  H  A  I  N  A  I  V  R  S  P  R  G  G  A  R  R  H  A         p.940

          .         .         .         .         .         .       g.39254
 GAGCTGTCCTTCGTGTTCCTCACGGACGGCGTCACGGGCAACGACAGTCTGCACGAGTCG       c.2880
 E  L  S  F  V  F  L  T  D  G  V  T  G  N  D  S  L  H  E  S         p.960

          .         .         .         .         .         .       g.39314
 GCGCACTCCATGCGCAAGCAGAACGTGGTACCCACCGTGCTGGCCTTGGGCAGCGACGTG       c.2940
 A  H  S  M  R  K  Q  N  V  V  P  T  V  L  A  L  G  S  D  V         p.980

          .         .         .         .         .         .       g.39374
 GACATGGACGTGCTCACCACGCTCAGCCTGGGTGACCGCGCCGCCGTGTTCCACGAGAAG       c.3000
 D  M  D  V  L  T  T  L  S  L  G  D  R  A  A  V  F  H  E  K         p.1000

          .         .         .         .         .         .       g.39434
 GACTATGACAGCCTGGCGCAACCCGGCTTCTTCGACCGCTTCATCCGCTGGATCTGCTAG       c.3060
 D  Y  D  S  L  A  Q  P  G  F  F  D  R  F  I  R  W  I  C  X         p.1019

          .         .         .         .         .         .       g.39494
 cgccgccgcccgggccccgcagtcgagggtcgtgagcccaccccgtccatggtgctaagc       c.*60

          .         .         .         .         .         .       g.39554
 gggcccgggtcccacacggccagcaccgctgctcactcggacgacgccctgggcctgcac       c.*120

          .         .         .         .         .         .       g.39614
 ctctccagctcctcccacggggtccccgtagccccggcccccgcccagccccaggtctcc       c.*180

          .         .         .         .         .         .       g.39674
 ccaggccctccgcaggctgcccggcctccctccccctgcagccatcccaaggctcctgac       c.*240

          .         .         .         .         .                 g.39731
 ctacctggcccctgagctctggagcaagccctgacccaataaaggctttgaacccat          c.*297

 (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 2 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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