visual system homeobox 1 (VSX1) - coding DNA reference sequence

(used for variant description)

(last modified November 26, 2020)

This file was created to facilitate the description of sequence variants on transcript NM_014588.5 in the VSX1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_008101.3, covering VSX1 transcript NM_014588.5.

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

 (upstream sequence)
                     .         .         .         .                g.5043
                  cctagaatgggggtggggtggggtggggtgggctggacagaag       c.-241

 .         .         .         .         .         .                g.5103
 agaggaggagaaggaggtgactgaggggactgcagctgggtgggcggtaaccgaggggag       c.-181

 .         .         .         .         .         .                g.5163
 gggaactggtggcgtccccatctcgcggggtccggaacggcgacgcgcccgcgcccagct       c.-121

 .         .         .         .         .         .                g.5223
 gattggagcccttcaggcctcccgcgcccgaccggcagcccaatcctataaagcttcctc       c.-61

 .         .         .         .         .         .                g.5283
 taagctgggccctccgcaaacgggatccagagaggctcgcgccttgcttgctaaggaacc       c.-1

          .         .         .         .         .         .       g.5343
 ATGACCGGCCGGGACTCGCTTTCCGACGGGCGCACTAGCAGCAGGGCGCTGGTGCCTGGC       c.60
 M  T  G  R  D  S  L  S  D  G  R  T  S  S  R  A  L  V  P  G         p.20

          .         .         .         .         .         .       g.5403
 GGTTCCCCTAGGGGCTCGCGCCCCCGGGGCTTCGCCATCACGGACCTGCTGGGCTTGGAG       c.120
 G  S  P  R  G  S  R  P  R  G  F  A  I  T  D  L  L  G  L  E         p.40

          .         .         .         .         .         .       g.5463
 GCCGAGCTGCCGGCGCCCGCTGGCCCAGGACAGGGATCTGGCTGCGAGGGTCCGGCAGTC       c.180
 A  E  L  P  A  P  A  G  P  G  Q  G  S  G  C  E  G  P  A  V         p.60

          .         .         .         .         .         .       g.5523
 GCGCCGTGCCCGGGCCCGGGGCTTGACGGCTCCAGCCTGGCGCGTGGGGCCCTACCGCTG       c.240
 A  P  C  P  G  P  G  L  D  G  S  S  L  A  R  G  A  L  P  L         p.80

          .         .         .         .         .         .       g.5583
 GGACTCGGCCTCCTCTGTGGCTTCGGCACGCAGCCGCCGGCGGCCGCTCGAGCACCCTGC       c.300
 G  L  G  L  L  C  G  F  G  T  Q  P  P  A  A  A  R  A  P  C         p.100

          .         .         .         .         .         .       g.5643
 CTGCTCCTAGCGGACGTGCCGTTCCTGCCGCCCAGGGGCCCCGAGCCCGCTGCCCCGCTG       c.360
 L  L  L  A  D  V  P  F  L  P  P  R  G  P  E  P  A  A  P  L         p.120

          .         .         .         .         .         .       g.5703
 GCTCCCAGCCGTCCGCCGCCTGCGCTCGGCCGCCAGAAGCGCAGCGACAGCGTCTCCACG       c.420
 A  P  S  R  P  P  P  A  L  G  R  Q  K  R  S  D  S  V  S  T         p.140

      | 02   .         .         .         .         .         .    g.7921
 TCCG | ATGAGGACAGCCAGTCTGAAGACAGGAATGACCTAAAGGCATCCCCCACCTTGGGC    c.480
 S  D |   E  D  S  Q  S  E  D  R  N  D  L  K  A  S  P  T  L  G      p.160

          .         .    | 03    .         .         .         .    g.8464
 AAGAGGAAGAAGCGGCGGCACAG | GACAGTTTTCACTGCTCACCAGCTGGAAGAGTTGGAG    c.540
 K  R  K  K  R  R  H  R  |  T  V  F  T  A  H  Q  L  E  E  L  E      p.180

          .         .         .         .         .         .       g.8524
 AAGGCATTCAGCGAGGCCCACTACCCTGATGTGTATGCCCGAGAAATGCTGGCTGTGAAA       c.600
 K  A  F  S  E  A  H  Y  P  D  V  Y  A  R  E  M  L  A  V  K         p.200

          .         .        | 04.         .         .         .    g.9547
 ACTGAGCTCCCCGAAGACCGGATACAG | GTCTGGTTTCAAAACCGCAGGGCCAAATGGCGC    c.660
 T  E  L  P  E  D  R  I  Q   | V  W  F  Q  N  R  R  A  K  W  R      p.220

          .         .         .         .         .         .       g.9607
 AAGCGGGAGAAGCGCTGGGGCGGCAGCAGCGTGATGGCCGAGTACGGGCTGTACGGGGCC       c.720
 K  R  E  K  R  W  G  G  S  S  V  M  A  E  Y  G  L  Y  G  A         p.240

          .         .         .         .         .         .       g.9667
 ATGGTGCGCCACTGCATCCCGCTGCCAGACTCCGTGCTCAACTCCGCCGAGGGCGGCCTG       c.780
 M  V  R  H  C  I  P  L  P  D  S  V  L  N  S  A  E  G  G  L         p.260

          .         .         | 05         .         .         .    g.10861
 CTGGGCTCCTGCGCGCCCTGGCTCCTGG | GGATGCATAAAAAATCCATGGGGATGATAAGG    c.840
 L  G  S  C  A  P  W  L  L  G |   M  H  K  K  S  M  G  M  I  R      p.280

          .         .         .         .         .         .       g.10921
 AAGCCAGGAAGTGAAGATAAGTTGGCAGGACTCTGGGGCTCTGACCACTTCAAAGAAGGT       c.900
 K  P  G  S  E  D  K  L  A  G  L  W  G  S  D  H  F  K  E  G         p.300

          .         .         .         .         .         .       g.10981
 TCTAGCCAGAGTGAGTCAGGATCACAGAGAGGCTCAGATAAAGTGAGCCCTGAGAATGGC       c.960
 S  S  Q  S  E  S  G  S  Q  R  G  S  D  K  V  S  P  E  N  G         p.320

          .         .         .         .         .         .       g.11041
 TTGGAAGATGTGGCTATTGACCTCTCCAGCTCTGCCCGGCAGGAGACCAAGAAAGTGCAC       c.1020
 L  E  D  V  A  I  D  L  S  S  S  A  R  Q  E  T  K  K  V  H         p.340

          .         .         .         .         .         .       g.11101
 CCTGGGGCTGGTGCTCAAGGAGGCTCCAACTCCACGGCACTGGAGGGGCCCCAGCCAGGG       c.1080
 P  G  A  G  A  Q  G  G  S  N  S  T  A  L  E  G  P  Q  P  G         p.360

          .                                                         g.11119
 AAGGTGGGAGCCACATGA                                                 c.1098
 K  V  G  A  T  X                                                   p.365

          .         .         .         .         .         .       g.11179
 gacccacaggtcccactgtcaaaggctgaaaatgtgcatattcctcactggcattttcca       c.*60

          .         .         .         .         .         .       g.11239
 aaagacaaaaattgtccaagacatatactctcagtttgattttcttctgacaatgtcaag       c.*120

          .         .         .         .         .         .       g.11299
 ataaaatgcaatgccacttgctttaagaggacagatgagtgacctagggaaaattctatt       c.*180

          .         .         .         .         .         .       g.11359
 tcattctagaatggaaacggttccttaatggcactttaaccagttaacttggtgcaaaac       c.*240

          .         .         .         .         .         .       g.11419
 ttttgattctcttttgtagcttgagcagggaggatccgaagttcaaaaatgatttcactg       c.*300

          .         .         .         .         .         .       g.11479
 ctgggcatcatttgagatgtgtggttcaatgtactgtatagatgaataggttaggtctga       c.*360

          .         .         .         .         .         .       g.11539
 tgtcctcattctcaattaggaaatataaaattgtttaatatccagaagaatctgatatca       c.*420

          .         .         .         .         .         .       g.11599
 tcatagtgaagactccatacagacacatgaatgaattatattgtctttaccttgaacttg       c.*480

          .         .         .         .         .         .       g.11659
 gccttggatatttcaattttcttgttagggagtaattttgtgttttcttgagtgtcactt       c.*540

          .         .         .         .         .         .       g.11719
 gataggctatgcatattggaattcaaagaaacccatactctagtcgtttctgcatttcct       c.*600

          .         .         .         .         .         .       g.11779
 ttaaaaatagcatgggatcatatttaaacaattgttggatagctggaaacagtgttttta       c.*660

          .         .         .         .         .         .       g.11839
 ggtcagaccaggcttttggtctttcaaaatttgtgattgaaagcactttagtgacttgga       c.*720

          .         .         .         .         .         .       g.11899
 ttttgtaaatctttcctttcctgcgtttcctttgccatttatttattctttaaaaataaa       c.*780

          .         .         .         .                           g.11944
 cattttgtggtgtgtttacttttcaaggcactcctctattacaca                      c.*825

 (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 Visual system homeobox 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.