S-antigen; retina and pineal gland (arrestin) (SAG) - coding DNA reference sequence

(used for variant description)

(last modified January 31, 2017)

This file was created to facilitate the description of sequence variants on transcript NM_000541.4 in the SAG gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_009116.1, covering SAG transcript NM_000541.4.

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

 (upstream sequence)
                                         .         .                g.5028
                                 gtcagctgggtgactcatacatctgtga       c.-361

 .         .         .         .         .         .                g.5088
 gaccctccgtatggagaccggggcggggggtgttgcttaatgcttagaactgctgaaact       c.-301

 .         .         .         .         .         .                g.5148
 accagttcactgtctcagcactaatccaactctgctccttaagtgggatttggcttttag       c.-241

 .         .         .         .         .         .                g.5208
 acattgagacctggatgctgggcatcctcgctagatcccctacaaattccccacatacgt       c.-181

 .         .         .         .         .         .                g.5268
 aggccaggagcctcagcggtgccccttcaggctcatctggcaagacggtaccagcttgct       c.-121

 .         .         .         .         .         .                g.5328
 cagaacaggggctggctattcatcatctcagagcatagagaccctctccttgccacccgg       c.-61

 .         .         .         .  | 02      .         .             g.6527
 cccttcccacctggttggtgacaaatcacaag | gtggtagaagttgccagggacagataac    c.-1

          .         .         .         .         .         .       g.6587
 ATGGCAGCCAGCGGGAAGACCAGCAAGTCCGAACCGAACCATGTTATCTTCAAGAAGATC       c.60
 M  A  A  S  G  K  T  S  K  S  E  P  N  H  V  I  F  K  K  I         p.20

          .      | 03  .         .         .         .         .    g.13457
 TCCCGGGACAAATCG | GTGACCATCTACCTGGGGAACAGAGACTACATAGACCATGTCAGC    c.120
 S  R  D  K  S   | V  T  I  Y  L  G  N  R  D  Y  I  D  H  V  S      p.40

          .       | 04 .         .         .         .         .    g.16132
 CAAGTCCAGCCTGTGG | ATGGTGTCGTGTTGGTTGATCCTGATCTTGTGAAGGGAAAGAAA    c.180
 Q  V  Q  P  V  D |   G  V  V  L  V  D  P  D  L  V  K  G  K  K      p.60

   | 05      .         .         .         .         .         .    g.18026
 G | TGTATGTCACTCTGACCTGCGCCTTCCGCTATGGCCAAGAGGACATTGACGTGATCGGC    c.240
 V |   Y  V  T  L  T  C  A  F  R  Y  G  Q  E  D  I  D  V  I  G      p.80

          .         .         .         .         .         .       g.18086
 TTGACCTTCCGCAGGGACCTGTACTTCTCCCGGGTCCAGGTGTATCCTCCTGTGGGGGCC       c.300
 L  T  F  R  R  D  L  Y  F  S  R  V  Q  V  Y  P  P  V  G  A         p.100

          .         .         .         .         .         .       g.18146
 GCGAGCACCCCCACAAAACTGCAAGAGAGCCTGCTTAAAAAGCTGGGGAGCAACACGTAC       c.360
 A  S  T  P  T  K  L  Q  E  S  L  L  K  K  L  G  S  N  T  Y         p.120

          .      | 06  .         .         .         .         .    g.20328
 CCCTTTCTCCTGACG | TTTCCTGACTACTTGCCCTGTTCAGTGATGTTGCAGCCAGCTCCA    c.420
 P  F  L  L  T   | F  P  D  Y  L  P  C  S  V  M  L  Q  P  A  P      p.140

          .      | 07  .         .         .         .         .    g.24503
 CAAGATTCAGGGAAG | TCCTGTGGGGTTGACTTTGAGGTCAAAGCATTCGCCACAGACAGC    c.480
 Q  D  S  G  K   | S  C  G  V  D  F  E  V  K  A  F  A  T  D  S      p.160

          .         .         .   | 08     .         .         .    g.25843
 ACCGATGCCGAAGAGGACAAAATCCCCAAGAA | GAGCTCCGTGCGATTACTGATCCGCAAA    c.540
 T  D  A  E  E  D  K  I  P  K  K  |  S  S  V  R  L  L  I  R  K      p.180

          .         .         .         .         .         .       g.25903
 GTACAGCATGCCCCACTTGAGATGGGTCCCCAGCCCCGAGCTGAGGCGGCCTGGCAGTTC       c.600
 V  Q  H  A  P  L  E  M  G  P  Q  P  R  A  E  A  A  W  Q  F         p.200

          .         .         .         .         | 09         .    g.26842
 TTCATGTCTGACAAGCCCCTGCACCTTGCGGTCTCTCTCAACAAAGAG | ATCTATTTCCAT    c.660
 F  M  S  D  K  P  L  H  L  A  V  S  L  N  K  E   | I  Y  F  H      p.220

          .         .         .         .         .         .       g.26902
 GGGGAGCCCATCCCTGTGACCGTGACTGTCACCAATAACACAGAGAAGACCGTGAAGAAG       c.720
 G  E  P  I  P  V  T  V  T  V  T  N  N  T  E  K  T  V  K  K         p.240

          .    | 10    .         .         .         .         .    g.29024
 ATTAAAGCATTCG | TGGAACAGGTGGCCAATGTGGTTCTCTACTCGAGTGATTATTACGTC    c.780
 I  K  A  F  V |   E  Q  V  A  N  V  V  L  Y  S  S  D  Y  Y  V      p.260

          .         .       | 11 .         .         .         .    g.32333
 AAGCCCGTGGCTATGGAGGAAGCGCA | AGAAAAAGTGCCACCAAACAGCACTTTGACCAAG    c.840
 K  P  V  A  M  E  E  A  Q  |  E  K  V  P  P  N  S  T  L  T  K      p.280

          .         .         .         .         .         .       g.32393
 ACGCTGACGCTGCTGCCCTTGCTGGCTAACAATCGAGAAAGGAGAGGCATTGCCCTGGAT       c.900
 T  L  T  L  L  P  L  L  A  N  N  R  E  R  R  G  I  A  L  D         p.300

          .         .         .         .     | 12   .         .    g.36029
 GGGAAAATCAAGCACGAGGACACAAACCTTGCCTCCAGCACCAT | CATTAAGGAGGGCATA    c.960
 G  K  I  K  H  E  D  T  N  L  A  S  S  T  I  |  I  K  E  G  I      p.320

          .         .         .         .         .         .       g.36089
 GACCGGACCGTCCTGGGAATCCTGGTGTCTTACCAGATCAAGGTGAAGCTCACAGTGTCA       c.1020
 D  R  T  V  L  G  I  L  V  S  Y  Q  I  K  V  K  L  T  V  S         p.340

    | 13     .         .       | 14 .         .         .         . g.39642
 GG | CTTTCTGGGAGAGCTCACCTCCAG | TGAAGTCGCCACTGAGGTCCCATTCCGCCTCATG c.1080
 G  |  F  L  G  E  L  T  S  S  |  E  V  A  T  E  V  P  F  R  L  M   p.360

          .         .   | 15     .   | 16     .         .         . g.44172
 CACCCTCAGCCTGAGGACCCAG | CTAAGGAAAG | TTATCAGGATGCAAATTTAGTTTTTGAG c.1140
 H  P  Q  P  E  D  P  A |   K  E  S  |  Y  Q  D  A  N  L  V  F  E   p.380

          .         .         .         .         .         .       g.44232
 GAGTTTGCTCGCCATAATCTGAAAGATGCAGGAGAAGCTGAGGAGGGGAAGAGAGACAAG       c.1200
 E  F  A  R  H  N  L  K  D  A  G  E  A  E  E  G  K  R  D  K         p.400

          .                                                         g.44250
 AATGACGTTGATGAGTGA                                                 c.1218
 N  D  V  D  E  X                                                   p.405

          .         .         .         .         .         .       g.44310
 agatgtcggctcaggatgccggaaaatgacctgtagttaccagtgcaacgagcaaagccc       c.*60

          .         .         .         .         .         .       g.44370
 cacagtttagtcctttggagttatgctgcgtatgaaaggatgagtcttcttccgagaaat       c.*120

          .         .                                               g.44393
 aaagcttgtttgttctcccctgg                                            c.*143

 (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 S-antigen; retina and pineal gland (arrestin) 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.