SRY (sex determining region Y)-box 4 (SOX4) - coding DNA reference sequence

(used for variant description)

(last modified February 12, 2019)
This file was created to facilitate the description of sequence variants on transcript NM_003107.2 in the SOX4 gene based on a coding DNA reference sequence following the HGVS recommendations.
The sequence was taken from NG_029166.1, covering SOX4 transcript NM_003107.2.
Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                                                   .                g.5014
                                               attggggtctgctc       c.-781

 .         .         .         .         .         .                g.5074
 taagctgcagcaagagaaactgtgtgtgaggggaagaggcctgtttcgctgtcgggtctc       c.-721

 .         .         .         .         .         .                g.5134
 tagttcttgcacgctctttaagagtctgcactggaggaactcctgccattaccagctccc       c.-661

 .         .         .         .         .         .                g.5194
 ttcttgcagaagggagggggaaacatacatttattcatgccagtctgttgcatgcaggct       c.-601

 .         .         .         .         .         .                g.5254
 ttttggcttcctaccttgcaacaaaataattgcaccaactccttagtgccgattccgccc       c.-541

 .         .         .         .         .         .                g.5314
 acagagagtcctggagccacagtcttttttgctttgcattgtaggagagggactaagtgc       c.-481

 .         .         .         .         .         .                g.5374
 tagagactatgtcgctttcctgagctaccgagagcgctcgtgaactggaatcaactgctt       c.-421

 .         .         .         .         .         .                g.5434
 cagggaaaaagaaaaaaaaaaaaaaaagacttgcctgggaggccgcgagaaacttgcatt       c.-361

 .         .         .         .         .         .                g.5494
 ggaagcttcagcaaccagcattcgagaaactcctctctactttagcacggtctccagact       c.-301

 .         .         .         .         .         .                g.5554
 cagccgagagacagcaaactgcagcgcggtgagagagcgagagagagggagagagagact       c.-241

 .         .         .         .         .         .                g.5614
 ctccagcctgggaactataactcctctgcgagaggcggagaactccttccccaaatcttt       c.-181

 .         .         .         .         .         .                g.5674
 tggggacttttctctctttacccacctccgcccctgcgaggagttgaggggccagttcgg       c.-121

 .         .         .         .         .         .                g.5734
 ccgccgcgcgcgtcttcccgttcggcgtgtgcttggcccggggaaccgggagggcccggc       c.-61

 .         .         .         .         .         .                g.5794
 gatcgcgcggcggccgccgcgagggtgtgagcgcgcgtgggcgcccgccgagccgaggcc       c.-1

          .         .         .         .         .         .       g.5854
 ATGGTGCAGCAAACCAACAATGCCGAGAACACGGAAGCGCTGCTGGCCGGCGAGAGCTCG       c.60
 M  V  Q  Q  T  N  N  A  E  N  T  E  A  L  L  A  G  E  S  S         p.20

          .         .         .         .         .         .       g.5914
 GACTCGGGCGCCGGCCTCGAGCTGGGAATCGCCTCCTCCCCCACGCCCGGCTCCACCGCC       c.120
 D  S  G  A  G  L  E  L  G  I  A  S  S  P  T  P  G  S  T  A         p.40

          .         .         .         .         .         .       g.5974
 TCCACGGGCGGCAAGGCCGACGACCCGAGCTGGTGCAAGACCCCGAGTGGGCACATCAAG       c.180
 S  T  G  G  K  A  D  D  P  S  W  C  K  T  P  S  G  H  I  K         p.60

          .         .         .         .         .         .       g.6034
 CGACCCATGAACGCCTTCATGGTGTGGTCGCAGATCGAGCGGCGCAAGATCATGGAGCAG       c.240
 R  P  M  N  A  F  M  V  W  S  Q  I  E  R  R  K  I  M  E  Q         p.80

          .         .         .         .         .         .       g.6094
 TCGCCCGACATGCACAACGCCGAGATCTCCAAGCGGCTGGGCAAACGCTGGAAGCTGCTC       c.300
 S  P  D  M  H  N  A  E  I  S  K  R  L  G  K  R  W  K  L  L         p.100

          .         .         .         .         .         .       g.6154
 AAAGACAGCGACAAGATCCCTTTCATTCGAGAGGCGGAGCGGCTGCGCCTCAAGCACATG       c.360
 K  D  S  D  K  I  P  F  I  R  E  A  E  R  L  R  L  K  H  M         p.120

          .         .         .         .         .         .       g.6214
 GCTGACTACCCCGACTACAAGTACCGGCCCAGGAAGAAGGTGAAGTCCGGCAACGCCAAC       c.420
 A  D  Y  P  D  Y  K  Y  R  P  R  K  K  V  K  S  G  N  A  N         p.140

          .         .         .         .         .         .       g.6274
 TCCAGCTCCTCGGCCGCCGCCTCCTCCAAGCCGGGGGAGAAGGGAGACAAGGTCGGTGGC       c.480
 S  S  S  S  A  A  A  S  S  K  P  G  E  K  G  D  K  V  G  G         p.160

          .         .         .         .         .         .       g.6334
 AGTGGCGGGGGCGGCCATGGGGGCGGCGGCGGCGGCGGGAGCAGCAACGCGGGGGGAGGA       c.540
 S  G  G  G  G  H  G  G  G  G  G  G  G  S  S  N  A  G  G  G         p.180

          .         .         .         .         .         .       g.6394
 GGCGGCGGTGCGAGTGGCGGCGGCGCCAACTCCAAACCGGCGCAGAAAAAGAGCTGCGGC       c.600
 G  G  G  A  S  G  G  G  A  N  S  K  P  A  Q  K  K  S  C  G         p.200

          .         .         .         .         .         .       g.6454
 TCCAAAGTGGCGGGCGGCGCGGGCGGTGGGGTTAGCAAACCGCACGCCAAGCTCATCCTG       c.660
 S  K  V  A  G  G  A  G  G  G  V  S  K  P  H  A  K  L  I  L         p.220

          .         .         .         .         .         .       g.6514
 GCAGGCGGCGGCGGCGGCGGGAAAGCAGCGGCTGCCGCCGCCGCCTCCTTCGCCGCCGAA       c.720
 A  G  G  G  G  G  G  K  A  A  A  A  A  A  A  S  F  A  A  E         p.240

          .         .         .         .         .         .       g.6574
 CAGGCGGGGGCCGCCGCCCTGCTGCCCCTGGGCGCCGCCGCCGACCACCACTCGCTGTAC       c.780
 Q  A  G  A  A  A  L  L  P  L  G  A  A  A  D  H  H  S  L  Y         p.260

          .         .         .         .         .         .       g.6634
 AAGGCGCGGACTCCCAGCGCCTCGGCCTCCGCCTCCTCGGCAGCCTCGGCCTCCGCAGCG       c.840
 K  A  R  T  P  S  A  S  A  S  A  S  S  A  A  S  A  S  A  A         p.280

          .         .         .         .         .         .       g.6694
 CTCGCGGCCCCGGGCAAGCACCTGGCGGAGAAGAAGGTGAAGCGCGTCTACCTGTTCGGC       c.900
 L  A  A  P  G  K  H  L  A  E  K  K  V  K  R  V  Y  L  F  G         p.300

          .         .         .         .         .         .       g.6754
 GGCCTGGGCACGTCGTCGTCGCCCGTGGGCGGCGTGGGCGCGGGAGCCGACCCCAGCGAC       c.960
 G  L  G  T  S  S  S  P  V  G  G  V  G  A  G  A  D  P  S  D         p.320

          .         .         .         .         .         .       g.6814
 CCCCTGGGCCTGTACGAGGAGGAGGGCGCGGGCTGCTCGCCCGACGCGCCCAGCCTGAGC       c.1020
 P  L  G  L  Y  E  E  E  G  A  G  C  S  P  D  A  P  S  L  S         p.340

          .         .         .         .         .         .       g.6874
 GGCCGCAGCAGCGCCGCCTCGTCCCCCGCCGCCGGCCGCTCGCCCGCCGACCACCGCGGC       c.1080
 G  R  S  S  A  A  S  S  P  A  A  G  R  S  P  A  D  H  R  G         p.360

          .         .         .         .         .         .       g.6934
 TACGCCAGCCTGCGCGCCGCCTCGCCCGCCCCGTCCAGCGCGCCCTCGCACGCGTCCTCC       c.1140
 Y  A  S  L  R  A  A  S  P  A  P  S  S  A  P  S  H  A  S  S         p.380

          .         .         .         .         .         .       g.6994
 TCGGCCTCGTCCCACTCCTCCTCTTCCTCCTCCTCGGGCTCCTCGTCCTCCGACGACGAG       c.1200
 S  A  S  S  H  S  S  S  S  S  S  S  G  S  S  S  S  D  D  E         p.400

          .         .         .         .         .         .       g.7054
 TTCGAAGACGACCTGCTCGACCTGAACCCCAGCTCAAACTTTGAGAGCATGTCCCTGGGC       c.1260
 F  E  D  D  L  L  D  L  N  P  S  S  N  F  E  S  M  S  L  G         p.420

          .         .         .         .         .         .       g.7114
 AGCTTCAGTTCGTCGTCGGCGCTCGACCGGGACCTGGATTTTAACTTCGAGCCCGGCTCC       c.1320
 S  F  S  S  S  S  A  L  D  R  D  L  D  F  N  F  E  P  G  S         p.440

          .         .         .         .         .         .       g.7174
 GGCTCGCACTTCGAGTTCCCGGACTACTGCACGCCCGAGGTGAGCGAGATGATCTCGGGA       c.1380
 G  S  H  F  E  F  P  D  Y  C  T  P  E  V  S  E  M  I  S  G         p.460

          .         .         .         .                           g.7219
 GACTGGCTCGAGTCCAGCATCTCCAACCTGGTTTTCACCTACTGA                      c.1425
 D  W  L  E  S  S  I  S  N  L  V  F  T  Y  X                        p.474

          .         .         .         .         .         .       g.7279
 agggcgcgcaggcagggagaagggccggggggggtaggagaggagaaaaaaaaagtgaaa       c.*60

          .         .         .         .         .         .       g.7339
 aaaagaaacgaaaaggacagacgaagagtttaaagagaaaagggaaaaaagaaagaaaaa       c.*120

          .         .         .         .         .         .       g.7399
 gtaagcagggctggcttcgcccgcgttctcgtcgtcggatcaaggagcgcggcggcgttt       c.*180

          .         .         .         .         .         .       g.7459
 tggacccgcgctcccatcccccaccttcccgggccggggacccactctgcccagccggag       c.*240

          .         .         .         .         .         .       g.7519
 ggacgcggaggaggaagagggtagacaggggcgacctgtgattgttgttattgatgttgt       c.*300

          .         .         .         .         .         .       g.7579
 tgttgatggcaaaaaaaaaaaagcgacttcgagtttgctcccctttgcttgaagagaccc       c.*360

          .         .         .         .         .         .       g.7639
 cctcccccttccaacgagcttccggacttgtctgcacccccagcaagaaggcgagttagt       c.*420

          .         .         .         .         .         .       g.7699
 tttctagagacttgaaggagtctcccccttcctgcatcaccaccttggttttgttttatt       c.*480

          .         .         .         .         .         .       g.7759
 ttgcttcttggtcaagaaaggaggggagaacccagcgcacccctccccccctttttttaa       c.*540

          .         .         .         .         .         .       g.7819
 acgcgtgatgaagacagaaggctccggggtgacgaatttggccgatggcagatgttttgg       c.*600

          .         .         .         .         .         .       g.7879
 gggaacgccgggactgagagactccacgcaggcgaattcccgtttggggcttttttttcc       c.*660

          .         .         .         .         .         .       g.7939
 tccctcttttccccttgccccctctgcagccggaggaggagatgttgaggggaggaggcc       c.*720

          .         .         .         .         .         .       g.7999
 agccagtgtgaccggcgctaggaaatgacccgagaaccccgttggaagcgcagcagcggg       c.*780

          .         .         .         .         .         .       g.8059
 agctaggggcgggggcggaggaggacacgaactggaagggggttcacggtcaaactgaaa       c.*840

          .         .         .         .         .         .       g.8119
 tggatttgcacgttggggagctggcggcggcggctgctgggcctccgccttcttttctac       c.*900

          .         .         .         .         .         .       g.8179
 gtgaaatcagtgaggtgagacttcccagaccccggaggcgtggaggagaggagactgttt       c.*960

          .         .         .         .         .         .       g.8239
 gatgtggtacaggggcagtcagtggagggcgagtggtttcggaaaaaaaaaaagaaaaaa       c.*1020

          .         .         .         .         .         .       g.8299
 agaaaaaaaaagaaaaaaaaaagatttttttcttctcttaatcggaatcgtgatggtgtt       c.*1080

          .         .         .         .         .         .       g.8359
 ggattatttcaatggtggggttaatatagcatgttatcctgtctatcttttaaagatttc       c.*1140

          .         .         .         .         .         .       g.8419
 tgtataagactgttgagcagtttttaaaatagtgtaggataatataaaaagcagatagat       c.*1200

          .         .         .         .         .         .       g.8479
 ggcgctatgtttgattcctacaacgaaattatcaccagctttttttcattcttaactctt       c.*1260

          .         .         .         .         .         .       g.8539
 taaaggattcaaacgcaactcaaatctgtgctggactttaaaaaaacaattcaggaccaa       c.*1320

          .         .         .         .         .         .       g.8599
 attttttctcagtgtgtgtgtttattccttataggtgtaaatgagaagacgtgttttttt       c.*1380

          .         .         .         .         .         .       g.8659
 ccttcaccgatgctccatcctcgtatttctttttccttgtaaatgtaatcagatgccatt       c.*1440

          .         .         .         .         .         .       g.8719
 ttatatgtggacgtatttatactggccaaacatattttttcttttgtccctttttttctt       c.*1500

          .         .         .         .         .         .       g.8779
 tcctttctttttacttcctttatttctttattccttccttttcctttttttctttttttt       c.*1560

          .         .         .         .         .         .       g.8839
 ttctttttttttttttttttttggtagttgttgttacccacgccattttacgtctccttc       c.*1620

          .         .         .         .         .         .       g.8899
 actgaagggctagagttttaacttttaattttttatatttaaatgtagacttttgacact       c.*1680

          .         .         .         .         .         .       g.8959
 tttaaaaaacaaaaaaagacaagagagatgaaaacgtttgattattttctcagtgtattt       c.*1740

          .         .         .         .         .         .       g.9019
 ttgtaaaaaatatataaagggggtgttaatcggtgtaaatcgctgtttggatttcctgat       c.*1800

          .         .         .         .         .         .       g.9079
 tttataacagggcggctggttaatatctcacacagtttaaaaaatcagcccctaatttct       c.*1860

          .         .         .         .         .         .       g.9139
 ccatgtttacacttcaatctgcaggcttcttaaagtgacagtatcccttaacctgccacc       c.*1920

          .         .         .         .         .         .       g.9199
 agtgtccaccctccggcccccgtcttgtaaaaaggggaggagaattagccaaacactgta       c.*1980

          .         .         .         .         .         .       g.9259
 agcttttaagaaaaacaaagttttaaacgaaatactgctctgtccagaggctttaaaact       c.*2040

          .         .         .         .         .         .       g.9319
 ggtgcaattacagcaaaaagggattctgtagctttaacttgtaaaccacatcttttttgc       c.*2100

          .         .         .         .         .         .       g.9379
 actttttttataagcaaaaacgtgccgtttaaaccactggatctatctaaatgccgattt       c.*2160

          .         .         .         .         .         .       g.9439
 gagttcgcgacactatgtactgcgtttttcattcttgtatttgactatttaatcctttct       c.*2220

          .         .         .         .         .         .       g.9499
 acttgtcgctaaatataattgttttagtcttatggcatgatgatagcatatgtgttcagg       c.*2280

          .         .         .         .         .         .       g.9559
 tttatagctgttgtgtttaaaaattgaaaaaagtggaaaacatctttgtacatttaagtc       c.*2340

          .         .         .         .         .         .       g.9619
 tgtattataataagcaaaaagattgtgtgtatgtatgtttaatataacatgacaggcact       c.*2400

          .         .         .         .         .         .       g.9679
 aggacgtctgcctttttaaggcagttccgttaagggtttttgtttttaaacttttttttg       c.*2460

          .         .         .         .         .         .       g.9739
 ccatccatcctgtgcaatatgccgtgtagaatatttgtcttaaaattcaaggccacaaaa       c.*2520

          .         .         .         .         .         .       g.9799
 acaatgtttgggggaaaaaaaagaaaaaatcatgccagctaatcatgtcaagttcactgc       c.*2580

          .         .         .         .         .         .       g.9859
 ctgtcagattgttgatatataccttctgtaaataactttttttgagaaggaaataaaatc       c.*2640

          .         .                                               g.9879
 agctggaactgaaccctaaa                                               c.*2660

 (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 SRY (sex determining region Y)-box 4 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.