SIX homeobox 1 (SIX1) - coding DNA reference sequence

(used for variant description)

(last modified January 23, 2022)

This file was created to facilitate the description of sequence variants on transcript NM_005982.3 in the SIX1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000014.8, covering SIX1 transcript NM_005982.3.

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

 (upstream sequence)
                                                                    g.5008
                                                     cggaggca       c.-241

 .         .         .         .         .         .                g.5068
 gcaaggccttaaaggctactgagtgcgccggccgttccgtgtccagaacctcccctactc       c.-181

 .         .         .         .         .         .                g.5128
 ctccgccttctcttccttggccgcccaccgccaagttccgactccggttttcgcctttgc       c.-121

 .         .         .         .         .         .                g.5188
 aaagcctaaggaggaggttaggaacagccgcgcccccctccctgcggccgccgccccctg       c.-61

 .         .         .         .         .         .                g.5248
 cctctcggctctgctccctgccgcgtgcgcctgggccgtgcgccccggcaggccccagcc       c.-1

          .         .         .         .         .         .       g.5308
 ATGTCGATGCTGCCGTCGTTTGGCTTTACGCAGGAGCAAGTGGCGTGCGTGTGCGAGGTT       c.60
 M  S  M  L  P  S  F  G  F  T  Q  E  Q  V  A  C  V  C  E  V         p.20

          .         .         .         .         .         .       g.5368
 CTGCAGCAAGGCGGAAACCTGGAGCGCCTGGGCAGGTTCCTGTGGTCACTGCCCGCCTGC       c.120
 L  Q  Q  G  G  N  L  E  R  L  G  R  F  L  W  S  L  P  A  C         p.40

          .         .         .         .         .         .       g.5428
 GACCACCTGCACAAGAACGAGAGCGTACTCAAGGCCAAGGCGGTGGTCGCCTTCCACCGC       c.180
 D  H  L  H  K  N  E  S  V  L  K  A  K  A  V  V  A  F  H  R         p.60

          .         .         .         .         .         .       g.5488
 GGCAACTTCCGTGAGCTCTACAAGATCCTGGAGAGCCACCAGTTCTCGCCTCACAACCAC       c.240
 G  N  F  R  E  L  Y  K  I  L  E  S  H  Q  F  S  P  H  N  H         p.80

          .         .         .         .         .         .       g.5548
 CCCAAACTGCAGCAACTGTGGCTGAAGGCGCATTACGTGGAGGCCGAGAAGCTGCGCGGC       c.300
 P  K  L  Q  Q  L  W  L  K  A  H  Y  V  E  A  E  K  L  R  G         p.100

          .         .         .         .         .         .       g.5608
 CGACCCCTGGGCGCCGTGGGCAAATATCGGGTGCGCCGAAAATTTCCACTGCCGCGCACC       c.360
 R  P  L  G  A  V  G  K  Y  R  V  R  R  K  F  P  L  P  R  T         p.120

          .         .         .         .         .         .       g.5668
 ATCTGGGACGGCGAGGAGACCAGCTACTGCTTCAAGGAGAAGTCGAGGGGTGTCCTGCGG       c.420
 I  W  D  G  E  E  T  S  Y  C  F  K  E  K  S  R  G  V  L  R         p.140

          .         .         .         .         .         .       g.5728
 GAGTGGTACGCGCACAATCCCTACCCATCGCCGCGTGAGAAGCGGGAGCTGGCCGAGGCC       c.480
 E  W  Y  A  H  N  P  Y  P  S  P  R  E  K  R  E  L  A  E  A         p.160

          .         .         .         .         .         .       g.5788
 ACCGGCCTCACCACCACCCAGGTCAGCAACTGGTTTAAGAACCGGAGGCAAAGAGACCGG       c.540
 T  G  L  T  T  T  Q  V  S  N  W  F  K  N  R  R  Q  R  D  R         p.180

          .         . | 02       .         .         .         .    g.7900
 GCCGCGGAGGCCAAGGAAAG | GGAGAACACCGAAAACAATAACTCCTCCTCCAACAAGCAG    c.600
 A  A  E  A  K  E  R  |  E  N  T  E  N  N  N  S  S  S  N  K  Q      p.200

          .         .         .         .         .         .       g.7960
 AACCAACTCTCTCCTCTGGAAGGGGGCAAGCCGCTCATGTCCAGCTCAGAAGAGGAATTC       c.660
 N  Q  L  S  P  L  E  G  G  K  P  L  M  S  S  S  E  E  E  F         p.220

          .         .         .         .         .         .       g.8020
 TCACCTCCCCAAAGTCCAGACCAGAACTCGGTCCTTCTGCTGCAGGGCAATATGGGCCAC       c.720
 S  P  P  Q  S  P  D  Q  N  S  V  L  L  L  Q  G  N  M  G  H         p.240

          .         .         .         .         .         .       g.8080
 GCCAGGAGCTCAAACTATTCTCTCCCGGGCTTAACAGCCTCGCAGCCCAGTCACGGCCTG       c.780
 A  R  S  S  N  Y  S  L  P  G  L  T  A  S  Q  P  S  H  G  L         p.260

          .         .         .         .         .         .       g.8140
 CAGACCCACCAGCATCAGCTCCAAGACTCTCTGCTCGGCCCCCTCACCTCCAGTCTGGTG       c.840
 Q  T  H  Q  H  Q  L  Q  D  S  L  L  G  P  L  T  S  S  L  V         p.280

          .                                                         g.8155
 GACTTGGGGTCCTAA                                                    c.855
 D  L  G  S  X                                                      p.284

          .         .         .         .         .         .       g.8215
 gtggggagggactggggcctcgaagggattcctggagcagcaaccactgcagcgactagg       c.*60

          .         .         .         .         .         .       g.8275
 gacacttgtaaatagaaatcaggaacatttttgcagcttgtttctggagttgtttgcgca       c.*120

          .         .         .         .         .         .       g.8335
 taaaggaatggtggactttcacaaatatctttttaaaaatcaaaaccaacagcgatctca       c.*180

          .         .         .         .         .         .       g.8395
 agcttaatctcctcttctctccaactctttccacttttgcattttccttcccaatgcaga       c.*240

          .         .         .         .         .         .       g.8455
 gatcagggaaaaaaaaaaaaaaaaacccaaacaaacaaaagcacccaggcacccagtctg       c.*300

          .         .         .         .         .         .       g.8515
 agttctgggcaactgatacgcctgtttcagcagcctttcttttttttcaatgaatgggaa       c.*360

          .         .         .         .         .         .       g.8575
 ttgcaaatcaactggattttcattatttccttttaatttatatatggagaaatgtgaaga       c.*420

          .         .         .         .         .         .       g.8635
 gggaaaggaaatggaaagagaaagagaaagggagataaaaatagtgaaaataagagcctc       c.*480

          .         .         .         .         .         .       g.8695
 caggctcagaagaactgattacattcttaaggtgaacaggaaaaatacaatctataactt       c.*540

          .         .         .         .         .         .       g.8755
 tctttgatgaggaaaaattaagtttacatttttcatatttagtgttaaacaatttaatgt       c.*600

          .         .         .         .         .         .       g.8815
 agattaaaataaaagaccagtattaggaggaaaaaacaagtgcctaaatgtcttaatgct       c.*660

          .         .         .         .         .         .       g.8875
 ctctatgtgagacagaaatagacgtgaccattagtaatgcaactatttttgtcaaattta       c.*720

          .         .         .         .         .         .       g.8935
 gtgggattttttggttgttgtttgttttcttgggttttttttttttaaatgacaaactct       c.*780

          .         .         .         .         .         .       g.8995
 aaaaatgtaccaatgtgaaaaaacactttcctgaatgccattactcatgccctcaaagct       c.*840

          .         .         .         .         .         .       g.9055
 ttcatatctgtagcctactcctgtaaagggtttctcctgtttctagtttctagtttgcaa       c.*900

          .         .         .         .         .         .       g.9115
 aggtatgccaacgaatctggcaacctggtatttgttactaaaacagcatgtgttttcagg       c.*960

          .         .         .         .         .         .       g.9175
 tttcttttctattgtacctaaagcagtctaaattaaaacttagtagaacaccaggagtat       c.*1020

          .         .         .         .         .         .       g.9235
 gattctgtttctgaaaggtgagtggtgtattgctgtcattgggccctattttttttttta       c.*1080

          .         .         .         .         .         .       g.9295
 aatatatttttctttcttacttaatggtggctgtgaattgcagggtactttgaaggccat       c.*1140

          .         .         .         .         .         .       g.9355
 catctgaaccaagagtagtaactagattaattatatgacagaaagagtgaatttagcctt       c.*1200

          .         .         .         .         .         .       g.9415
 ggggtatttattaacttctattatttagatatgcaattttgtttaccactatctcttcac       c.*1260

          .         .         .         .         .         .       g.9475
 agcattcatatgttaactaagctcttttgtgttaacaagtttatgacaagactgtgaaag       c.*1320

          .         .         .         .         .         .       g.9535
 taaaaataatttatctgcttgaagacaaaaaagggaaggagaacaaggatagaaacattg       c.*1380

          .         .         .         .         .         .       g.9595
 tgaattaatttgtacaaatagaaagcagaccagcaggacaggagctcttttgcagtgctg       c.*1440

          .         .         .         .         .         .       g.9655
 ccggatggtgtctagaaaaatcccagtaatcatgtaggctccatattatttttgcctggg       c.*1500

          .         .         .         .         .         .       g.9715
 gcaaaatgatgtatcttctgtatttagcttttaaaattagtgaaacaaatggcattattt       c.*1560

          .         .                                               g.9739
 attaaaattctactcaggataaca                                           c.*1584

 (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 SIX 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.