syntrophin, alpha 1 (SNTA1) - coding DNA reference sequence

(used for variant description)

(last modified June 11, 2016)

This file was created to facilitate the description of sequence variants on transcript NM_003098.2 in the SNTA1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_011622.1, covering SNTA1 transcript NM_003098.2.

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

 (upstream sequence)
                               .         .         .                g.5032
                             cccttctgacccaccccgctaggtagtcccac       c.-241

 .         .         .         .         .         .                g.5092
 acggcggccctcggctcccgggccccgccccggcctcctgcatttgcccgaggccccctc       c.-181

 .         .         .         .         .         .                g.5152
 cccagcactggccacaccccagggtagccccgcccccagagctcctcccccagcggccgg       c.-121

 .         .         .         .         .         .                g.5212
 ggtagggtggcggctggcccagccgggcccccgctgccctctgccctgggcgcttggtcg       c.-61

 .         .         .         .         .         .                g.5272
 gagcgggctgggcaaagcgggacagggcgagcgcggcggcccgggggctcggaggcgaag       c.-1

          .         .         .         .         .         .       g.5332
 ATGGCGTCCGGCAGGCGCGCCCCGCGCACCGGGCTGCTGGAGCTGCGCGCCGGGGCGGGC       c.60
 M  A  S  G  R  R  A  P  R  T  G  L  L  E  L  R  A  G  A  G         p.20

          .         .         .         .         .         .       g.5392
 TCGGGGGCCGGCGGCGAGCGATGGCAGCGGGTGCTGCTGAGTCTGGCGGAGGACGTGCTG       c.120
 S  G  A  G  G  E  R  W  Q  R  V  L  L  S  L  A  E  D  V  L         p.40

          .         .         .         .         .         .       g.5452
 ACCGTGAGCCCCGCCGACGGCGACCCTGGTCCCGAGCCCGGCGCTCCGCGGGAGCAGGAG       c.180
 T  V  S  P  A  D  G  D  P  G  P  E  P  G  A  P  R  E  Q  E         p.60

          .         .         .         .         .         .       g.5512
 CCCGCGCAGCTCAACGGCGCCGCGGAGCCGGGCGCCGGGCCCCCGCAGCTGCCAGAGGCG       c.240
 P  A  Q  L  N  G  A  A  E  P  G  A  G  P  P  Q  L  P  E  A         p.80

          .         .         .         .         .         .       g.5572
 CTACTGCTCCAGCGGCGCCGCGTGACGGTGCGCAAGGCCGACGCCGGTGGGCTGGGCATC       c.300
 L  L  L  Q  R  R  R  V  T  V  R  K  A  D  A  G  G  L  G  I         p.100

          . | 02       .         .         .         .         .    g.9916
 AGCATCAAAG | GCGGCCGGGAGAACAAGATGCCTATTCTCATTTCCAAGATCTTCAAGGGA    c.360
 S  I  K  G |   G  R  E  N  K  M  P  I  L  I  S  K  I  F  K  G      p.120

          .         .         .         .         .         .       g.9976
 TTGGCAGCTGACCAGACAGAGGCCCTTTTTGTGGGGGATGCCATCCTGTCTGTGAATGGG       c.420
 L  A  A  D  Q  T  E  A  L  F  V  G  D  A  I  L  S  V  N  G         p.140

          .         .         .         .         .         .       g.10036
 GAAGACTTGTCCTCTGCTACCCATGATGAGGCGGTGCAGGTCCTCAAGAAGACAGGCAAG       c.480
 E  D  L  S  S  A  T  H  D  E  A  V  Q  V  L  K  K  T  G  K         p.160

          .       | 03 .         .         .         .         .    g.31013
 GAGGTGGTGCTGGAGG | TCAAGTATATGAAGGACGTCTCACCGTATTTCAAGAACTCTACT    c.540
 E  V  V  L  E  V |   K  Y  M  K  D  V  S  P  Y  F  K  N  S  T      p.180

          .         .         .         .         .         .       g.31073
 GGTGGGACCTCGGTCGGCTGGGACTCACCTCCTGCCTCACCCCTTCAGCGGCAGCCTTCC       c.600
 G  G  T  S  V  G  W  D  S  P  P  A  S  P  L  Q  R  Q  P  S         p.200

          .         .         .         .         .         .       g.31133
 TCCCCTGGCCCCACACCCCGGAACTTCAGCGAGGCCAAACACATGTCCTTGAAGATGGCA       c.660
 S  P  G  P  T  P  R  N  F  S  E  A  K  H  M  S  L  K  M  A         p.220

          .         .         .         .  | 04      .         .    g.36129
 TATGTCTCGAAGAGGTGCACCCCCAATGACCCGGAGCCCAG | GTATCTGGAGATCTGCTCG    c.720
 Y  V  S  K  R  C  T  P  N  D  P  E  P  R  |  Y  L  E  I  C  S      p.240

          .         .         .         .         .         .       g.36189
 GCAGATGGTCAAGACACCCTCTTCCTGAGGGCCAAGGATGAGGCTAGTGCGAGGTCGTGG       c.780
 A  D  G  Q  D  T  L  F  L  R  A  K  D  E  A  S  A  R  S  W         p.260

          .         .         .         .         .         .       g.36249
 GCGACTGCCATCCAAGCCCAGGTCAATACTCTGACGCCGCGGGTCAAGGATGAGCTGCAG       c.840
 A  T  A  I  Q  A  Q  V  N  T  L  T  P  R  V  K  D  E  L  Q         p.280

          .         .         .         .         .         .       g.36309
 GCACTGTTGGCAGCCACCAGCACAGCTGGGAGCCAGGACATCAAGCAGATTGGCTGGCTA       c.900
 A  L  L  A  A  T  S  T  A  G  S  Q  D  I  K  Q  I  G  W  L         p.300

           | 05        .         .         .         .         .    g.36517
 ACTGAGCAG | CTGCCCAGTGGGGGCACAGCCCCCACCCTGGCCCTGCTAACTGAAAAGGAA    c.960
 T  E  Q   | L  P  S  G  G  T  A  P  T  L  A  L  L  T  E  K  E      p.320

          .         .         .         .         .         .       g.36577
 CTGCTCCTCTACTTGTCTCTCCCCGAGACCCGCGAGGCCCTGAGCCGGCCAGCCCGTACT       c.1020
 L  L  L  Y  L  S  L  P  E  T  R  E  A  L  S  R  P  A  R  T         p.340

          .         . | 06       .         .         .         .    g.38601
 GCCCCACTCATCGCCACCAG | ACTGGTGCACTCAGGCCCCTCCAAGGGCTCAGTGCCCTAC    c.1080
 A  P  L  I  A  T  R  |  L  V  H  S  G  P  S  K  G  S  V  P  Y      p.360

          .         .         .         .         .         .       g.38661
 GATGCAGAGCTCTCTTTTGCCCTGCGCACGGGCACGCGTCACGGTGTGGACACTCACCTG       c.1140
 D  A  E  L  S  F  A  L  R  T  G  T  R  H  G  V  D  T  H  L         p.380

          .         .         .         .         .         .       g.38721
 TTCAGCGTGGAGTCACCGCAGGAGCTGGCTGCCTGGACCCGCCAGCTTGTGGATGGCTGT       c.1200
 F  S  V  E  S  P  Q  E  L  A  A  W  T  R  Q  L  V  D  G  C         p.400

          .         .         .        | 07.         .         .    g.40027
 CACCGGGCCGCCGAGGGTGTGCAGGAGGTGTCTACAG | CCTGCACGTGGAATGGGCGTCCC    c.1260
 H  R  A  A  E  G  V  Q  E  V  S  T  A |   C  T  W  N  G  R  P      p.420

          .         .         .         .         .         .       g.40087
 TGCAGCCTGTCTGTGCACATCGACAAGGGCTTCACACTGTGGGCGGCTGAGCCAGGTGCA       c.1320
 C  S  L  S  V  H  I  D  K  G  F  T  L  W  A  A  E  P  G  A         p.440

          .         .         .         .         .         .       g.40147
 GCCCGAGCTGTGCTCCTGCGACAGCCCTTCGAGAAGCTGCAGATGTCTTCAGATGACGGT       c.1380
 A  R  A  V  L  L  R  Q  P  F  E  K  L  Q  M  S  S  D  D  G         p.460

          .         .         .         .      | 08  .         .    g.40308
 GCCAGTCTCCTTTTCCTGGATTTTGGAGGTGCTGAAGGCGAGATC | CAGCTGGACCTGCAC    c.1440
 A  S  L  L  F  L  D  F  G  G  A  E  G  E  I   | Q  L  D  L  H      p.480

          .         .         .         .         .         .       g.40368
 TCGTGTCCCAAAACCATAGTCTTCATCATCCACTCCTTCCTGTCGGCCAAAGTCACCCGC       c.1500
 S  C  P  K  T  I  V  F  I  I  H  S  F  L  S  A  K  V  T  R         p.500

          .                                                         g.40386
 CTCGGGCTGTTGGCCTAG                                                 c.1518
 L  G  L  L  A  X                                                   p.505

          .         .         .         .         .         .       g.40446
 aagtcgccggatgcactagccctgaagaggggtgtccatgacatggcctgagctgggcct       c.*60

          .         .         .         .         .         .       g.40506
 ccaccgactgcctgctcacccctgggctgagggaagggagaggagaggaacaagggcctc       c.*120

          .         .         .         .         .         .       g.40566
 cgaaaccccaaccctgagggagactggattggtcttggggcccaggacccagacgcagga       c.*180

          .         .         .         .         .         .       g.40626
 cagagtggactctgcctgtgatggggtggccttcctgctgcccccctccaccagtgcctt       c.*240

          .         .         .         .         .         .       g.40686
 ttgcagagagatattttgtgtacacagaagccattccgagtctgggacctgcccctgtgc       c.*300

          .         .         .         .         .         .       g.40746
 ggatcctgaccccagccaacagctgagctgccgggcctcctcgaggcccctaagccaccc       c.*360

          .         .         .         .         .         .       g.40806
 ccagaggtcccatctgaagctggagtaccctggggtcagcagcaagagaaagaagaggag       c.*420

          .         .         .         .         .         .       g.40866
 attttctgtttgtttttcccctcagccctgccaccgtggggagtctggtttttctcttca       c.*480

          .         .         .         .         .         .       g.40926
 tcctgtctctctcctccttactcttggataaataaacagcctgtgagcacacaggcagcc       c.*540

          .                                                         g.40936
 cggcccagtg                                                         c.*550

 (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 Syntrophin, 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.