torsin family 1, member A (torsin A) (TOR1A) - coding DNA reference sequence

(used for variant description)

(last modified April 8, 2014)

This file was created to facilitate the description of sequence variants on transcript NM_000113.2 in the TOR1A gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000009.11, covering TOR1A transcript NM_000113.2.

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

 (upstream sequence)
                                                   .                g.5017
                                            gaaccggaagcgtgggt       c.-61

 .         .         .         .         .         .                g.5077
 ctggcggctgcaccggttcgcggtcggcgcgagaacaagcagggtggcgcgggtccgggc       c.-1

          .         .         .         .         .         .       g.5137
 ATGAAGCTGGGCCGGGCCGTGCTGGGCCTGCTGCTGCTGGCGCCGTCCGTGGTGCAGGCG       c.60
 M  K  L  G  R  A  V  L  G  L  L  L  L  A  P  S  V  V  Q  A         p.20

          .         .         .         .         .         .       g.5197
 GTGGAGCCCATCAGCCTGGGACTGGCCCTGGCCGGCGTCCTCACCGGCTACATCTACCCG       c.120
 V  E  P  I  S  L  G  L  A  L  A  G  V  L  T  G  Y  I  Y  P         p.40

          .         .         .         .         .         | 02    g.6318
 CGTCTCTACTGCCTCTTCGCCGAGTGCTGCGGGCAGAAGCGGAGCCTTAGCCGGGAGG | CA    c.180
 R  L  Y  C  L  F  A  E  C  C  G  Q  K  R  S  L  S  R  E  A |       p.60

          .         .         .         .         .         .       g.6378
 CTGCAGAAGGATCTGGACGACAACCTCTTTGGACAGCATCTTGCAAAGAAAATCATCTTA       c.240
 L  Q  K  D  L  D  D  N  L  F  G  Q  H  L  A  K  K  I  I  L         p.80

          .         .         .         .         .         .       g.6438
 AATGCCGTGTTTGGTTTCATAAACAACCCAAAGCCCAAGAAACCTCTCACGCTCTCCCTG       c.300
 N  A  V  F  G  F  I  N  N  P  K  P  K  K  P  L  T  L  S  L         p.100

          .         .         .         .         .         .       g.6498
 CACGGGTGGACAGGCACCGGCAAAAATTTCGTCAGCAAGATCATCGCAGAGAATATTTAC       c.360
 H  G  W  T  G  T  G  K  N  F  V  S  K  I  I  A  E  N  I  Y         p.120

          .         .         .         .         .         .       g.6558
 GAGGGTGGTCTGAACAGTGACTATGTCCACCTGTTTGTGGCCACATTGCACTTTCCACAT       c.420
 E  G  G  L  N  S  D  Y  V  H  L  F  V  A  T  L  H  F  P  H         p.140

          .         .     | 03   .         .         .         .    g.10278
 GCTTCAAACATCACCTTGTACAAG | GATCAGTTACAGTTGTGGATTCGAGGCAACGTGAGT    c.480
 A  S  N  I  T  L  Y  K   | D  Q  L  Q  L  W  I  R  G  N  V  S      p.160

          .         .         .         .         .         .       g.10338
 GCCTGTGCGAGGTCCATCTTCATATTTGATGAAATGGATAAGATGCATGCAGGCCTCATA       c.540
 A  C  A  R  S  I  F  I  F  D  E  M  D  K  M  H  A  G  L  I         p.180

          .         .         .         .         .         .       g.10398
 GATGCCATCAAGCCTTTCCTCGACTATTATGACCTGGTGGATGGGGTCTCCTACCAGAAA       c.600
 D  A  I  K  P  F  L  D  Y  Y  D  L  V  D  G  V  S  Y  Q  K         p.200

          .         . | 04       .         .         .         .    g.10555
 GCCATGTTCATATTTCTCAG | CAATGCTGGAGCAGAAAGGATCACAGATGTGGCTTTGGAT    c.660
 A  M  F  I  F  L  S  |  N  A  G  A  E  R  I  T  D  V  A  L  D      p.220

          .         .         .         .         .         .       g.10615
 TTCTGGAGGAGTGGAAAGCAGAGGGAAGACATCAAGCTCAAAGACATTGAACACGCGTTG       c.720
 F  W  R  S  G  K  Q  R  E  D  I  K  L  K  D  I  E  H  A  L         p.240

          .         .         | 05         .         .         .    g.14972
 TCTGTGTCGGTTTTCAATAACAAGAACA | GTGGCTTCTGGCACAGCAGCTTAATTGACCGG    c.780
 S  V  S  V  F  N  N  K  N  S |   G  F  W  H  S  S  L  I  D  R      p.260

          .         .         .         .         .         .       g.15032
 AACCTCATTGATTATTTTGTTCCCTTCCTCCCCCTGGAATACAAACACCTAAAAATGTGT       c.840
 N  L  I  D  Y  F  V  P  F  L  P  L  E  Y  K  H  L  K  M  C         p.280

          .         .         .         .         .         .       g.15092
 ATCCGAGTGGAAATGCAGTCCCGAGGCTATGAAATTGATGAAGACATTGTAAGCAGAGTG       c.900
 I  R  V  E  M  Q  S  R  G  Y  E  I  D  E  D  I  V  S  R  V         p.300

          .         .         .         .         .         .       g.15152
 GCTGAGGAGATGACATTTTTCCCCAAAGAGGAGAGAGTTTTCTCAGATAAAGGCTGCAAA       c.960
 A  E  E  M  T  F  F  P  K  E  E  R  V  F  S  D  K  G  C  K         p.320

          .         .         .                                     g.15191
 ACGGTGTTCACCAAGTTAGATTATTACTACGATGATTGA                            c.999
 T  V  F  T  K  L  D  Y  Y  Y  D  D  X                              p.332

          .         .         .         .         .         .       g.15251
 cagtcatgattggcagccggagtcactgcctggagttggaaaagaaacaacactcagtcc       c.*60

          .         .         .         .         .         .       g.15311
 ttccacacttccacccccagctcctttccctggaagaggaatccagtgaatgttcctgtt       c.*120

          .         .         .         .         .         .       g.15371
 tgatgtgacaggaattctccctggcattgtttccaccccctggtgcctgcaggccaccca       c.*180

          .         .         .         .         .         .       g.15431
 gggaccacgggcgaggacgtgaagcctcccgaacacgcacagaaggaaggagccagctcc       c.*240

          .         .         .         .         .         .       g.15491
 cagcccactcatcgcagggctcatgattttttacaaattatgttttaattccaagtgttt       c.*300

          .         .         .         .         .         .       g.15551
 ctgtttcaaggaaggatgaataagttttattgaaaatgtggtaactttatttaaaatgat       c.*360

          .         .         .         .         .         .       g.15611
 ttttaacattatgagagactgctcagattctaagttgttggccttgtgtgtgtgtttttt       c.*420

          .         .         .         .         .         .       g.15671
 tttaagttctcatcattattacatagactgtgatgtatctttactggaaatgagcccaag       c.*480

          .         .         .         .         .         .       g.15731
 cacacatgcatggcatttgttccacaggagggcatccctggggatgtggctggagcatga       c.*540

          .         .         .         .         .         .       g.15791
 gccagctctgtcccaggatggtcccagcggatgctgccaggggcagtgaagtgtttaggt       c.*600

          .         .         .         .         .         .       g.15851
 gaaggacaagtaggtaagaggacgccttcaggcaccacagataagcctgaaacagcctct       c.*660

          .         .         .         .         .         .       g.15911
 ccaagggttttcaccttagcaacaatgggagctgtgggagtgattttggccacactgtca       c.*720

          .         .         .         .         .         .       g.15971
 acatttgttagaaccagtcttttgaaagaaaagtatttccaacttgtcacttgccagtca       c.*780

          .         .         .         .         .         .       g.16031
 ctccgttttgcaaaaggtggcccttcactgtccattccaaatagcccacacgtgctctct       c.*840

          .         .         .         .         .         .       g.16091
 gctggattctaaattatgtgaattttgccatattaaatcttcctcatttatactattatt       c.*900

          .         .         .         .         .         .       g.16151
 tgttacgttcaatcagaatccccgaaacctcctataaagcttagctgccccttctgagga       c.*960

          .         .         .         .         .         .       g.16211
 tgctgagaacggtgtctttctttataaatgcaaatggctaccgttttacaataaaatttt       c.*1020

          .                                                         g.16221
 gcatgtgcca                                                         c.*1030

 (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 Torsin family 1, member A (torsin A) 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.