ventral anterior homeobox 1 (VAX1) - coding DNA reference sequence

(used for variant description)

(last modified July 6, 2017)

This file was created to facilitate the description of sequence variants on transcript NM_001112704.1 in the VAX1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_012317.1, covering VAX1 transcript NM_001112704.1.

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

 (upstream sequence)
                                                                    g.5005
                                                        accag       c.-241

 .         .         .         .         .         .                g.5065
 actggccgcctctcggcgagcgcgccactctcccgtcgccgctgacccgcgcgcggccgc       c.-181

 .         .         .         .         .         .                g.5125
 cgaagcctccccgcggggacattcattcttgccccttgcctgtcgccgggccgggcgtac       c.-121

 .         .         .         .         .         .                g.5185
 gggccgcgttgtcgggggttttgtcccctttttcctcttttttttttccttctccgcccc       c.-61

 .         .         .         .         .         .                g.5245
 ccccccttttttttttttttgctttttttttcctttctgtttttgttgttgttcttgcct       c.-1

          .         .         .         .         .         .       g.5305
 ATGTTCGGGAAACCAGACAAAATGGACGTTCGATGCCACTCGGACGCCGAGGCTGCCCGG       c.60
 M  F  G  K  P  D  K  M  D  V  R  C  H  S  D  A  E  A  A  R         p.20

          .         .         .         .         .         .       g.5365
 GTCTCGAAGAACGCGCACAAGGAGAGTCGGGAGAGCAAGGGCGCGGAGGGGAACCTCCCA       c.120
 V  S  K  N  A  H  K  E  S  R  E  S  K  G  A  E  G  N  L  P         p.40

          .         .         .         .         .         .       g.5425
 GCCGCCTTCCTCAAGGAGCCGCAGGGCGCCTTCTCAGCGTCGGGCGCTGCTGAGGATTGT       c.180
 A  A  F  L  K  E  P  Q  G  A  F  S  A  S  G  A  A  E  D  C         p.60

          .         .         .         .         .         .       g.5485
 AACAAAAGTAAATCCAATTCCGCAGCGGACCCGGATTACTGCCGCCGGATCCTGGTCCGA       c.240
 N  K  S  K  S  N  S  A  A  D  P  D  Y  C  R  R  I  L  V  R         p.80

   | 02      .         .         .         .         .         .    g.6701
 G | ATGCCAAGGGGTCCATCCGAGAGATCATCCTGCCCAAGGGCCTGGACTTGGACCGGCCT    c.300
 D |   A  K  G  S  I  R  E  I  I  L  P  K  G  L  D  L  D  R  P      p.100

          .         .         .         .         .         .       g.6761
 AAGAGGACGCGCACGTCCTTCACCGCGGAGCAGCTCTATCGGCTGGAGATGGAGTTCCAG       c.360
 K  R  T  R  T  S  F  T  A  E  Q  L  Y  R  L  E  M  E  F  Q         p.120

          .         .         .         .         .         .       g.6821
 CGCTGCCAGTACGTGGTGGGCCGCGAGAGGACCGAGCTCGCCCGGCAGCTTAACCTCTCC       c.420
 R  C  Q  Y  V  V  G  R  E  R  T  E  L  A  R  Q  L  N  L  S         p.140

           | 03        .         .         .         .         .    g.8769
 GAGACCCAG | GTGAAGGTCTGGTTCCAGAACCGGCGCACCAAGCAGAAGAAGGACCAGGGC    c.480
 E  T  Q   | V  K  V  W  F  Q  N  R  R  T  K  Q  K  K  D  Q  G      p.160

          .         .         .         .         .         .       g.8829
 AAGGACTCGGAGCTACGCTCGGTGGTGTCGGAGACCGCGGCCACGTGCAGCGTGCTACGG       c.540
 K  D  S  E  L  R  S  V  V  S  E  T  A  A  T  C  S  V  L  R         p.180

          .         .         .         .         .         .       g.8889
 CTGCTGGAGCAGGGCCGCCTGTTGTCGCCGCCCGGCCTGCCTGCGCTGCTGCCGCCTTGC       c.600
 L  L  E  Q  G  R  L  L  S  P  P  G  L  P  A  L  L  P  P  C         p.200

          .         .         .         .         .         .       g.8949
 GCCACGGGCGCTCTCGGCTCAGCGCTGCGCGGGCCCAGCTTGCCGGCCCTGGGCGCGGGC       c.660
 A  T  G  A  L  G  S  A  L  R  G  P  S  L  P  A  L  G  A  G         p.220

          .         .         .         .         .         .       g.9009
 GCCGCTGCAGGCTCGGCCGCCGCAGCCGCCGCCGCCGCCCCGGGCCCAGCGGGCGCTGCA       c.720
 A  A  A  G  S  A  A  A  A  A  A  A  A  P  G  P  A  G  A  A         p.240

          .         .         .         .         .         .       g.9069
 TCCCCGCACCCGCCGGCTGTGGGCGGTGCTCCAGGTCCCGGGCCCGCCGGGCCGGGGGGA       c.780
 S  P  H  P  P  A  V  G  G  A  P  G  P  G  P  A  G  P  G  G         p.260

          .         .         .         .         .         .       g.9129
 TTGCACGCAGGCGCCCCGGCCGCGGGCCACAGCCTCTTCAGCCTGCCGGTGCCCTCGCTG       c.840
 L  H  A  G  A  P  A  A  G  H  S  L  F  S  L  P  V  P  S  L         p.280

          .         .         .         .         .         .       g.9189
 CTCGGCTCCGTCGCCAGCCGCCTGTCCTCCGCCCCGTTAACAATGGCTGGTTCGCTAGCT       c.900
 L  G  S  V  A  S  R  L  S  S  A  P  L  T  M  A  G  S  L  A         p.300

          .         .         .         .         .         .       g.9249
 GGGAATTTGCAAGAACTCTCCGCCCGATATCTGAGCTCCTCGGCCTTCGAGCCTTACTCC       c.960
 G  N  L  Q  E  L  S  A  R  Y  L  S  S  S  A  F  E  P  Y  S         p.320

          .         .         .         .                           g.9294
 CGGACCAACAATAAAGAAGGGGCCGAGAAAAAAGCGCTGGACTGA                      c.1005
 R  T  N  N  K  E  G  A  E  K  K  A  L  D  X                        p.334

          .         .         .         .         .         .       g.9354
 ttttaagtgtttccctgtatttatatttatagtatctattgtggtgatatttatggactc       c.*60

          .         .         .         .         .         .       g.9414
 acgcgcattaggtgcccagagctcctgcgctgggctcctggctcccaccaggcctctgac       c.*120

          .         .         .         .         .         .       g.9474
 agctctcctttcccactagactctgctaccaatttcatctcattcgggctattttttttt       c.*180

          .         .         .         .         .         .       g.9534
 tctactacctttcctctgagattcctccccaacccccaacttccttctgaatccaggagc       c.*240

          .         .         .         .         .         .       g.9594
 gatccaaagaattgggaaaaatgcccgagttagtcaacctgatgccctgaccccgtgccc       c.*300

          .         .         .         .         .         .       g.9654
 agcccaggagggaaaagactggttctaactccaaagcacaggacgtttgctctagatccg       c.*360

          .         .         .         .         .         .       g.9714
 cggctgctgcggctgctgccgctgccgactattcctaggaatatttgaaagaggaaaact       c.*420

          .         .         .         .         .         .       g.9774
 gcgcgcagaccccaggggcttccaggtttctttagaccaaaaaaggaggacgttccttcc       c.*480

          .         .         .         .         .         .       g.9834
 tcttgccagggaaaccagggcttgtgggagcccctgggccccgctttgcggacctctcgg       c.*540

          .         .         .         .         .         .       g.9894
 gatagtcggtacacaacacagcttcctggcgggcaaatcctgcggtttttctccccttta       c.*600

          .         .         .         .         .         .       g.9954
 gggcaactccaatcacaaccacccccgaccccaggaaacagtaacaaacgtcgtagtagg       c.*660

          .         .         .         .         .                 g.10012
 caacgacactgataaatttgatctaatcagcaataaaagcaattgctacgtaaaacca         c.*718

 (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 Ventral anterior 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.