collagen, type XIII, alpha 1 (COL13A1) - coding DNA reference sequence

(used for variant description)

(last modified March 19, 2017)

This file was created to facilitate the description of sequence variants on transcript NM_001130103.1 in the COL13A1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000010.10, covering COL13A1 transcript NM_001130103.1.

Please note that introns are available by clicking on the exon numbers above the sequence.

 (upstream sequence)
           .         .         .         .         .                g.5056
     aagtagcacggattgctcatccgatccgtgccgccgcagggagtgtgtcaagttac       c.-481

 .         .         .         .         .         .                g.5116
 agaggcgccggaatcggcccctgcgctcctcgccagccgccacgacccacctctgcccat       c.-421

 .         .         .         .         .         .                g.5176
 ggggccctccgtgtgcgccccttcgcccggggactgaaactgactggcccgggagacacg       c.-361

 .         .         .         .         .         .                g.5236
 aggcgcccagaaggactgacagcgcggcaccaactgctctgcagacacttgaagggaaag       c.-301

 .         .         .         .         .         .                g.5296
 actgggcggagagaaggagagccggtcagattcccctaactttcctggacttggaacgtt       c.-241

 .         .         .         .         .         .                g.5356
 cttcgaaataacttttttctcacctaggtgtaccccaattaccgctggttgtgctttttc       c.-181

 .         .         .         .         .         .                g.5416
 ggcacttcctctcctactgctaatttttccgtcctctttgccgggagcagcggaaaggga       c.-121

 .         .         .         .         .         .                g.5476
 cgttttccagcgatacaagccctttccccctgccccgcagtttggatagagccttttggc       c.-61

 .         .         .         .         .         .                g.5536
 agcggctgtcgcctttatttattctatttatttatttattggttctcaagacgcgagagg       c.-1

          .         .         .         .         .         .       g.5596
 ATGGTAGCGGAGCGCACCCACAAAGCGGCAGCCACCGGTGCCCGCGGCCCTGGGGAGTTG       c.60
 M  V  A  E  R  T  H  K  A  A  A  T  G  A  R  G  P  G  E  L         p.20

          .         .         .         .         .         .       g.5656
 GGCGCGCCCGGGACGGTGGCTCTGGTGGCGGCGCGGGCGGAGCGCGGCGCACGGCTGCCG       c.120
 G  A  P  G  T  V  A  L  V  A  A  R  A  E  R  G  A  R  L  P         p.40

          .         .         .         .         .         .       g.5716
 AGTCCAGGGTCGTGCGGGCTGCTGACGCTGGCCCTCTGCTCGCTGGCACTCAGCCTGCTC       c.180
 S  P  G  S  C  G  L  L  T  L  A  L  C  S  L  A  L  S  L  L         p.60

          .         .         .         .         .         .       g.5776
 GCCCACTTTCGGACGGCCGAGCTGCAGGCCCGGGTGCTGCGCCTGGAAGCGGAGCGCGGG       c.240
 A  H  F  R  T  A  E  L  Q  A  R  V  L  R  L  E  A  E  R  G         p.80

          .         .         .         .         .     | 02   .    g.25487
 GAGCAGCAAATGGAGACGGCTATTTTGGGACGAGTCAATCAACTGCTGGACGAG | AAATGG    c.300
 E  Q  Q  M  E  T  A  I  L  G  R  V  N  Q  L  L  D  E   | K  W      p.100

          .         .         .         .         .         .       g.25547
 AAGCTCCACTCAAGGAGGCGCCGGGAGGCCCCAAAGACATCTCCAGGATGTAACTGCCCA       c.360
 K  L  H  S  R  R  R  R  E  A  P  K  T  S  P  G  C  N  C  P         p.120

      | 03   .   | 04     .         .          | 05        .         . g.78261
 CCAG | GACCTCCT | GGTCCCACTGGAAGACCCGGACTCCCA | GGGGACAAAGGTGCCATTGGG c.420
 P  G |   P  P   | G  P  T  G  R  P  G  L  P   | G  D  K  G  A  I  G   p.140

          .      | 06  .         .         .         .         .    g.83660
 ATGCCTGGACGTGTG | GGGTCCCCCGGAGACGCTGGGCTGTCCATCATTGGTCCCCGCGGC    c.480
 M  P  G  R  V   | G  S  P  G  D  A  G  L  S  I  I  G  P  R  G      p.160

        | 07 .         .         .         .   | 08     .         . g.91434
 CCCCCT | GGTCAACCAGGAACTAGAGGTTTCCCTGGATTTCCG | GGTCCCATTGGGCTGGAC c.540
 P  P   | G  Q  P  G  T  R  G  F  P  G  F  P   | G  P  I  G  L  D   p.180

           | 09        .         .       | 10 .         .         . g.97688
 GGCAAACCG | GGCCACCCAGGACCAAAGGGCGACATG | GGTCTGACGGGTCCCCCAGGACAG c.600
 G  K  P   | G  H  P  G  P  K  G  D  M   | G  L  T  G  P  P  G  Q   p.200

     | 11    .         .         . | 12       .         .        | 13. g.100590
 CCG | GGACCCCAGGGACAAAAAGGAGAAAAG | GGTCAGTGTGGAGAGTACCCACACCGG | GAG c.660
 P   | G  P  Q  G  Q  K  G  E  K   | G  Q  C  G  E  Y  P  H  R   | E   p.220

          .         .         .         .         .     | 14   .    g.101815
 TGCCTAAGCAGCATGCCAGCAGCTCTGCGCTCCAGCCAAATAATTGCCCTGAAG | CTGCTG    c.720
 C  L  S  S  M  P  A  A  L  R  S  S  Q  I  I  A  L  K   | L  L      p.240

          .         .         .         .         .         .       g.101875
 CCTCTCCTCAATTCAGTGCGACTGGCTCCACCCCCGGTCATAAAAAGGCGGACGTTCCAG       c.780
 P  L  L  N  S  V  R  L  A  P  P  P  V  I  K  R  R  T  F  Q         p.260

  | 15       .         .         .         .         .         .    g.105920
  | GGCGAACAGAGCCAGGCCAGCATCCAAGGTCCACCAGGGCCCCCAGGCCCCCCTGGACCA    c.840
  | G  E  Q  S  Q  A  S  I  Q  G  P  P  G  P  P  G  P  P  G  P      p.280

          .         .         .         .         | 16         .    g.108057
 AGTGGACCTCTGGGGCACCCAGGACTGCCAGGGCCTATGGGGCCACCT | GGCTTACCTGGG    c.900
 S  G  P  L  G  H  P  G  L  P  G  P  M  G  P  P   | G  L  P  G      p.300

          .      | 17  .         .         .         .  | 18      . g.120410
 CCTCCTGGACCAAAG | GGAGACCCAGGGATCCAGGGCTACCACGGCCGGAAG | GGAGAACGG c.960
 P  P  G  P  K   | G  D  P  G  I  Q  G  Y  H  G  R  K   | G  E  R   p.320

          .         .         .       | 19 .         .         .    g.121421
 GGCATGCCAGGGATGCCAGGCAAGCATGGAGCCAAG | GGGGCGCCCGGAATTGCCGTGGCT    c.1020
 G  M  P  G  M  P  G  K  H  G  A  K   | G  A  P  G  I  A  V  A      p.340

           | 20        .         .       | 21 .         .         . g.125018
 GGGATGAAG | GGTGAGCCAGGGATCCCAGGAACCAAG | GGTGAGAAGGGGGCTGAAGGCTCC c.1080
 G  M  K   | G  E  P  G  I  P  G  T  K   | G  E  K  G  A  E  G  S   p.360

          .         .         . | 22       .         .         .    g.125850
 CCTGGGCTTCCTGGCCTCCTGGGGCAGAAG | GGAGAGAAAGGCGATGCTGGCAACTCCATT    c.1140
 P  G  L  P  G  L  L  G  Q  K   | G  E  K  G  D  A  G  N  S  I      p.380

          .         .         .         .         .        | 23.    g.126917
 GGAGGAGGCAGAGGGGAACCTGGCCCTCCAGGGCTCCCTGGGCCCCCAGGGCCAAAG | GGA    c.1200
 G  G  G  R  G  E  P  G  P  P  G  L  P  G  P  P  G  P  K   | G      p.400

          .         .         .         .         .  | 24      .    g.128084
 GAAGCAGGTGTCGATGGCCAGGTTGGCCCCCCAGGGCAGCCAGGAGACAAG | GGGGAGCGT    c.1260
 E  A  G  V  D  G  Q  V  G  P  P  G  Q  P  G  D  K   | G  E  R      p.420

          .         .         .       | 25 .         .         .    g.128940
 GGAGCAGCTGGAGAACAGGGACCAGATGGCCCCAAG | GGCTCCAAGGGAGAACCAGGGAAA    c.1320
 G  A  A  G  E  Q  G  P  D  G  P  K   | G  S  K  G  E  P  G  K      p.440

          .         .         .         .      | 26  .         .    g.130214
 GGAGAGATGGTGGATTACAATGGAAACATCAATGAGGCTCTCCAG | GAGATCCGGACGCTG    c.1380
 G  E  M  V  D  Y  N  G  N  I  N  E  A  L  Q   | E  I  R  T  L      p.460

           | 27        .         .         .         .         .    g.132100
 GCCTTGATG | GGGCCTCCTGGTCTTCCTGGGCAAATTGGCCCACCTGGAGCTCCAGGGATT    c.1440
 A  L  M   | G  P  P  G  L  P  G  Q  I  G  P  P  G  A  P  G  I      p.480

          .   | 28     .         .         .         .        | 29. g.133515
 CCAGGCCAGAAG | GGGGAGATTGGACTGCCAGGCCCTCCAGGACACGATGGGGAAAAG | GGA c.1500
 P  G  Q  K   | G  E  I  G  L  P  G  P  P  G  H  D  G  E  K   | G   p.500

          .         .         .         .         .         .       g.133575
 CCTCGCGGTAAACCAGGAGACATGGGCCCTCCTGGTCCCCAAGGCCCCCCAGGAAAGGAT       c.1560
 P  R  G  K  P  G  D  M  G  P  P  G  P  Q  G  P  P  G  K  D         p.520

          .         .         .         .         .         .       g.133635
 GGACCTCCAGGAGTGAAGGGAGAAAACGGGCACCCAGGGAGCCCAGGAGAGAAGGGGGAA       c.1620
 G  P  P  G  V  K  G  E  N  G  H  P  G  S  P  G  E  K  G  E         p.540

          .         .         . | 30       .         .         .    g.135702
 AAAGGGGAGACAGGACAAGCAGGCTCACCG | GGAGAGAAAGGAGAAGCCGGGGAGAAGGGC    c.1680
 K  G  E  T  G  Q  A  G  S  P   | G  E  K  G  E  A  G  E  K  G      p.560

          .      | 31  .         .         .         .        | 32. g.139871
 AATCCAGGAGCAGAG | GTTCCTGGGCTGCCAGGGCCAGAGGGGCCTCCCGGACCTCCG | GGG c.1740
 N  P  G  A  E   | V  P  G  L  P  G  P  E  G  P  P  G  P  P   | G   p.580

          .         .     | 33   .         .         .         .    g.140783
 CTCCAAGGTGTTCCTGGACCAAAG | GGGGAAGCAGGACTAGATGGAGCAAAAGGAGAGAAA    c.1800
 L  Q  G  V  P  G  P  K   | G  E  A  G  L  D  G  A  K  G  E  K      p.600

          .         .         .         .      | 34  .         .    g.144115
 GGCTTCCAGGGAGAAAAAGGAGACCGTGGTCCCCTGGGACTACCC | GGAGCTTCAGGTTTG    c.1860
 G  F  Q  G  E  K  G  D  R  G  P  L  G  L  P   | G  A  S  G  L      p.620

          .         .  | 35      .         .         .         .    g.147276
 GACGGCAGGCCTGGGCCACCG | GGTACTCCAGGACCAATTGGAGTTCCAGGCCCAGCGGGA    c.1920
 D  G  R  P  G  P  P   | G  T  P  G  P  I  G  V  P  G  P  A  G      p.640

          .      | 36  .         .         .         .         .    g.148828
 CCAAAGGGCGAGAGG | GGCAGCAAAGGAGACCCTGGGATGACAGGACCAACGGGAGCAGCT    c.1980
 P  K  G  E  R   | G  S  K  G  D  P  G  M  T  G  P  T  G  A  A      p.660

           | 37        .         .         .      | 38  .         . g.156009
 GGGCTTCCT | GGTTTACATGGACCACCCGGGGACAAGGGAAACCGG | GGGGAGAGGGGGAAG c.2040
 G  L  P   | G  L  H  G  P  P  G  D  K  G  N  R   | G  E  R  G  K   p.680

          .         .         .         .         .         .       g.156069
 AAAGGCTCTAGAGGGCCTAAAGGGGATAAGGGAGACCAAGGAGCGCCTGGATTAGATGCC       c.2100
 K  G  S  R  G  P  K  G  D  K  G  D  Q  G  A  P  G  L  D  A         p.700

          .   | 39     .         .         .         .  | 40        g.161820
 CCCTGCCCATTG | GGCGAAGATGGCTTACCAGTCCAAGGCTGCTGGAACAAG | TGA       c.2154
 P  C  P  L   | G  E  D  G  L  P  V  Q  G  C  W  N  K   | X         p.717

          .         .         .         .         .         .       g.161880
 tgcctctaaccttggattggcctgtgtgtgtgtttgtacatagaatatttatttttatac       c.*60

          .         .         .         .         .         .       g.161940
 agttttcactttttgaaaatgccagaagtatgatgcatcttacagattattaaaaaagaa       c.*120

          .         .         .         .         .         .       g.162000
 agaaaaacctgcatattttgtacagaaaatatcaacctcttcccttttgtttacaagatg       c.*180

          .         .         .         .         .         .       g.162060
 ttttgtataagcctatgtctctaatacattttttgtttggtcgtaatgtctgcatgatat       c.*240

          .         .         .         .         .         .       g.162120
 ttgtgcacatttattaagtatcgaagcttaataaattattgtgtcctggtgccaaagggg       c.*300

          .         .         .         .         .         .       g.162180
 gccagccagaactgaggtgctggctagctcatgtgtgaattcacataaatgtagaggtcc       c.*360

          .         .         .         .         .         .       g.162240
 atgatatttgctaagctaggtgtgtctaagagtattttaaacccttatggattttcatta       c.*420

          .         .                                               g.162267
 ttaaaggaaatgaaacatggcaattca                                        c.*447

 (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 10^th nucleotide is indicated by a "." above the sequence. The Collagen, type XIII, 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 10^th 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 variants, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.