opsin 1 (cone pigments), long-wave-sensitive (OPN1LW) - coding DNA reference sequence

(used for variant description)

(last modified March 14, 2018)

This file was created to facilitate the description of sequence variants on transcript NM_020061.4 in the OPN1LW gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_009105.2, covering OPN1LW transcript NM_020061.4.

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

 (upstream sequence)
                               .         .         .                g.5033
                            cggctgccgtcggggacagggctttccatagcc       c.-1

          .         .         .         .         .         .       g.5093
 ATGGCCCAGCAGTGGAGCCTCCAAAGGCTCGCAGGCCGCCATCCGCAGGACAGCTATGAG       c.60
 M  A  Q  Q  W  S  L  Q  R  L  A  G  R  H  P  Q  D  S  Y  E         p.20

          .         .         .         .         .   | 02     .    g.11411
 GACAGCACCCAGTCCAGCATCTTCACCTACACCAACAGCAACTCCACCAGAG | GCCCCTTC    c.120
 D  S  T  Q  S  S  I  F  T  Y  T  N  S  N  S  T  R  G |   P  F      p.40

          .         .         .         .         .         .       g.11471
 GAAGGCCCGAATTACCACATCGCTCCCAGATGGGTGTACCACCTCACCAGTGTCTGGATG       c.180
 E  G  P  N  Y  H  I  A  P  R  W  V  Y  H  L  T  S  V  W  M         p.60

          .         .         .         .         .         .       g.11531
 ATCTTTGTGGTCACTGCATCCGTCTTCACAAATGGGCTTGTGCTGGCGGCCACCATGAAG       c.240
 I  F  V  V  T  A  S  V  F  T  N  G  L  V  L  A  A  T  M  K         p.80

          .         .         .         .         .         .       g.11591
 TTCAAGAAGCTGCGCCACCCGCTGAACTGGATCCTGGTGAACCTGGCGGTCGCTGACCTA       c.300
 F  K  K  L  R  H  P  L  N  W  I  L  V  N  L  A  V  A  D  L         p.100

          .         .         .         .         .         .       g.11651
 GCAGAGACCGTCATCGCCAGCACTATCAGCATTGTGAACCAGGTCTCTGGCTACTTCGTG       c.360
 A  E  T  V  I  A  S  T  I  S  I  V  N  Q  V  S  G  Y  F  V         p.120

          .         .         .         .          | 03        .    g.13699
 CTGGGCCACCCTATGTGTGTCCTGGAGGGCTACACCGTCTCCCTGTGTG | GGATCACAGGT    c.420
 L  G  H  P  M  C  V  L  E  G  Y  T  V  S  L  C  G |   I  T  G      p.140

          .         .         .         .         .         .       g.13759
 CTCTGGTCTCTGGCCATCATTTCCTGGGAGAGGTGGCTGGTGGTGTGCAAGCCCTTTGGC       c.480
 L  W  S  L  A  I  I  S  W  E  R  W  L  V  V  C  K  P  F  G         p.160

          .         .         .         .         .         .       g.13819
 AATGTGAGATTTGATGCCAAGCTGGCCATCGTGGGCATTGCCTTCTCCTGGATCTGGTCT       c.540
 N  V  R  F  D  A  K  L  A  I  V  G  I  A  F  S  W  I  W  S         p.180

          .         .         .         | 04         .         .    g.15346
 GCTGTGTGGACAGCCCCGCCCATCTTTGGTTGGAGCAG | GTACTGGCCCCACGGCCTGAAG    c.600
 A  V  W  T  A  P  P  I  F  G  W  S  R  |  Y  W  P  H  G  L  K      p.200

          .         .         .         .         .         .       g.15406
 ACTTCATGCGGCCCAGACGTGTTCAGCGGCAGCTCGTACCCCGGGGTGCAGTCTTACATG       c.660
 T  S  C  G  P  D  V  F  S  G  S  S  Y  P  G  V  Q  S  Y  M         p.220

          .         .         .         .         .         .       g.15466
 ATTGTCCTCATGGTCACCTGCTGCATCATCCCACTCGCTATCATCATGCTCTGCTACCTC       c.720
 I  V  L  M  V  T  C  C  I  I  P  L  A  I  I  M  L  C  Y  L         p.240

          .         .     | 05   .         .         .         .    g.17080
 CAAGTGTGGCTGGCCATCCGAGCG | GTGGCAAAGCAGCAGAAAGAGTCTGAATCCACCCAG    c.780
 Q  V  W  L  A  I  R  A   | V  A  K  Q  Q  K  E  S  E  S  T  Q      p.260

          .         .         .         .         .         .       g.17140
 AAGGCAGAGAAGGAAGTGACGCGCATGGTGGTGGTGATGATCTTTGCGTACTGCGTCTGC       c.840
 K  A  E  K  E  V  T  R  M  V  V  V  M  I  F  A  Y  C  V  C         p.280

          .         .         .         .         .         .       g.17200
 TGGGGACCCTACACCTTCTTCGCATGCTTTGCTGCTGCCAACCCTGGTTACGCCTTCCAC       c.900
 W  G  P  Y  T  F  F  A  C  F  A  A  A  N  P  G  Y  A  F  H         p.300

          .         .         .         .         .         .       g.17260
 CCTTTGATGGCTGCCCTGCCGGCCTACTTTGCCAAAAGTGCCACTATCTACAACCCCGTT       c.960
 P  L  M  A  A  L  P  A  Y  F  A  K  S  A  T  I  Y  N  P  V         p.320

          .         .     | 06   .         .         .         .    g.19602
 ATCTATGTCTTTATGAACCGGCAG | TTTCGAAACTGCATCTTGCAGCTTTTCGGGAAGAAG    c.1020
 I  Y  V  F  M  N  R  Q   | F  R  N  C  I  L  Q  L  F  G  K  K      p.340

          .         .         .         .         .         .       g.19662
 GTTGACGATGGCTCTGAACTCTCCAGCGCCTCCAAAACGGAGGTCTCATCTGTGTCCTCG       c.1080
 V  D  D  G  S  E  L  S  S  A  S  K  T  E  V  S  S  V  S  S         p.360

          .                                                         g.19677
 GTATCGCCTGCATGA                                                    c.1095
 V  S  P  A  X                                                      p.364

          .         .         .         .         .         .       g.19737
 ggtctgcctcctacccatcccgcccaccggggctttggccacctctcctttccccctcct       c.*60

          .         .         .         .                           g.19783
 tctccatccctgtaaaataaatgtaatttatctttgccaaaaccaa                     c.*106

 (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 Opsin 1 (cone pigments), long-wave-sensitive 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.