orthodenticle homeobox 2 (OTX2) - coding DNA reference sequence

(used for variant description)

(last modified November 25, 2020)

This file was created to facilitate the description of sequence variants on transcript NM_021728.3 in the OTX2 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_008204.1, covering OTX2 transcript NM_021728.3.

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

 (upstream sequence)
                     .         .         .         .                g.5044
                 aaatctccctgagagcgggaccggcctcagctccaacacagcct       c.-241

 .         .         .         .         .         .       | 02     g.5257
 ccactgtgattaaaaataaaaattgctagagcagccctcactcgccacatctacttt | gat    c.-181

 .         .         .         .         .         .                g.5317
 agctggctatttggaatttaaaggatatttgactttttctaacctcccatgaggctgtaa       c.-121

 . | 03       .         .         .         .         .             g.9960
 g | ttccactgctccaaacccacccaccaaggactctgaacctgtccaccccgggcgcatca    c.-61

 .         .         .         .         .         .                g.10020
 agatcttccagctgggtacccccgatttgggccgactttgcacctccaaacaaccttagc       c.-1

          .         .         .         .         .         .       g.10080
 ATGATGTCTTATCTTAAGCAACCGCCTTACGCAGTCAATGGGCTGAGTCTGACCACTTCG       c.60
 M  M  S  Y  L  K  Q  P  P  Y  A  V  N  G  L  S  L  T  T  S         p.20

          .         .         .        | 04.         .         .    g.11136
 GGTATGGACTTGCTGCACCCCTCCGTGGGCTACCCGG | GGCCCTGGGCTTCTTGTCCCGCA    c.120
 G  M  D  L  L  H  P  S  V  G  Y  P  G |   P  W  A  S  C  P  A      p.40

          .         .         .         .         .         .       g.11196
 GCCACCCCCCGGAAACAGCGCCGGGAGAGGACGACGTTCACTCGGGCGCAGCTAGATGTG       c.180
 A  T  P  R  K  Q  R  R  E  R  T  T  F  T  R  A  Q  L  D  V         p.60

          .         .         .         .         .         .       g.11256
 CTGGAAGCACTGTTTGCCAAGACCCGGTACCCAGACATCTTCATGCGAGAGGAGGTGGCA       c.240
 L  E  A  L  F  A  K  T  R  Y  P  D  I  F  M  R  E  E  V  A         p.80

          .         .         .    | 05    .         .         .    g.13148
 CTGAAAATCAACTTGCCCGAGTCGAGGGTGCAG | GTATGGTTTAAGAATCGAAGAGCTAAG    c.300
 L  K  I  N  L  P  E  S  R  V  Q   | V  W  F  K  N  R  R  A  K      p.100

          .         .         .         .         .         .       g.13208
 TGCCGCCAACAACAGCAACAACAGCAGAATGGAGGTCAAAACAAAGTGAGACCTGCCAAA       c.360
 C  R  Q  Q  Q  Q  Q  Q  Q  N  G  G  Q  N  K  V  R  P  A  K         p.120

          .         .         .         .         .         .       g.13268
 AAGAAGACATCTCCAGCTCGGGAAGTGAGTTCAGAGAGTGGAACAAGTGGCCAATTCACT       c.420
 K  K  T  S  P  A  R  E  V  S  S  E  S  G  T  S  G  Q  F  T         p.140

          .         .         .         .         .         .       g.13328
 CCCCCCTCTAGCACCTCAGTCCCGACCATTGCCAGCAGCAGTGCTCCTGTGTCTATCTGG       c.480
 P  P  S  S  T  S  V  P  T  I  A  S  S  S  A  P  V  S  I  W         p.160

          .         .         .         .         .         .       g.13388
 AGCCCAGCTTCCATCTCCCCACTGTCAGATCCCTTGTCCACCTCCTCTTCCTGCATGCAG       c.540
 S  P  A  S  I  S  P  L  S  D  P  L  S  T  S  S  S  C  M  Q         p.180

          .         .         .         .         .         .       g.13448
 AGGTCCTATCCCATGACCTATACTCAGGCTTCAGGTTATAGTCAAGGATATGCTGGCTCA       c.600
 R  S  Y  P  M  T  Y  T  Q  A  S  G  Y  S  Q  G  Y  A  G  S         p.200

          .         .         .         .         .         .       g.13508
 ACTTCCTACTTTGGGGGCATGGACTGTGGATCATATTTGACCCCTATGCATCACCAGCTT       c.660
 T  S  Y  F  G  G  M  D  C  G  S  Y  L  T  P  M  H  H  Q  L         p.220

          .         .         .         .         .         .       g.13568
 CCCGGACCAGGGGCCACACTCAGTCCCATGGGTACCAATGCAGTCACCAGCCATCTCAAT       c.720
 P  G  P  G  A  T  L  S  P  M  G  T  N  A  V  T  S  H  L  N         p.240

          .         .         .         .         .         .       g.13628
 CAGTCCCCAGCTTCTCTTTCCACCCAGGGATATGGAGCTTCAAGCTTGGGTTTTAACTCA       c.780
 Q  S  P  A  S  L  S  T  Q  G  Y  G  A  S  S  L  G  F  N  S         p.260

          .         .         .         .         .         .       g.13688
 ACCACTGATTGCTTGGATTATAAGGACCAAACTGCCTCCTGGAAGCTTAACTTCAATGCT       c.840
 T  T  D  C  L  D  Y  K  D  Q  T  A  S  W  K  L  N  F  N  A         p.280

          .         .         .         .         .                 g.13742
 GACTGCTTGGATTATAAAGATCAGACATCCTCGTGGAAATTCCAGGTTTTGTGA             c.894
 D  C  L  D  Y  K  D  Q  T  S  S  W  K  F  Q  V  L  X               p.297

          .         .         .         .         .         .       g.13802
 agacctgtagaacctctttttgtgggtgatttttaaatatactgggctggacattccagt       c.*60

          .         .         .         .         .         .       g.13862
 tttagccaggcattggttaaaagagttagatgggatgatgctcagactcatctgatcaaa       c.*120

          .         .         .         .         .         .       g.13922
 gttccgagaggcatagaaggaaaaacgaagggccttagaggggcctacaaaccagcaaca       c.*180

          .         .         .         .         .         .       g.13982
 tgaaatggacaaaccaatctgcttaagatcctgtcatagttttagatcattggttatcct       c.*240

          .         .         .         .         .         .       g.14042
 gatttgcaaagtgatcaaaagcattctagccatgtgcaaccaaacaccaccaaaaataaa       c.*300

          .         .         .         .         .         .       g.14102
 atcaaacaaaactaagttgtgaaggaagggagggaaggtcatagccttcttaagcagagg       c.*360

          .         .         .         .         .         .       g.14162
 tgttccattgttttagccaatccttggttgaatcttaggaatgaacagtgtctcaagctc       c.*420

          .         .         .         .         .         .       g.14222
 attcacgtttcatgaccaactggtagttggcactgaaaaaacttttcagggctgtgtgaa       c.*480

          .         .         .         .         .         .       g.14282
 ttgtgtgactgattgtcctagatgcactactttatttaaaaaataatgttcataaggagt       c.*540

          .         .         .         .         .         .       g.14342
 caatatgtagtttaagagacaatcagtgtgtgtcttataaatggtacatctgtggttttt       c.*600

          .         .         .         .         .         .       g.14402
 aatctgtgctagacttcaaaactgtgatctcctgttattgtatgcaaccttgaactccac       c.*660

          .         .         .         .         .         .       g.14462
 ctctgcaggggttcttctgtgattaaataggttataattataagcaaaattcagagcaac       c.*720

          .         .         .         .         .         .       g.14522
 tgagtactgatctaaaaagattacctttggctggaggtgagctgcactgaaactttacga       c.*780

          .         .         .         .         .         .       g.14582
 caaaatgtctctggacaaagagagtcagagaagagaagcaaaaggacactaattcatctg       c.*840

          .         .         .         .         .         .       g.14642
 taatttactgttggtaagcctagcagtaaagagacattggtcaattgctctgaccctgat       c.*900

          .         .         .         .         .         .       g.14702
 gaattattaaactgagatcattgtcgtttatgcttgcagatgttaaatggaaaagttata       c.*960

          .         .         .         .         .         .       g.14762
 tatgcataaaccttttcttcctggatttggcagatatgtataattatattaaaatggttc       c.*1020

                                                                    g.14770
 tagcacaa                                                           c.*1028

 (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 Orthodenticle homeobox 2 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.