retinal degeneration 3 (RD3) - coding DNA reference sequence

(used for variant description)

(last modified January 25, 2024)

This file was created to facilitate the description of sequence variants on transcript NM_001164688.1 in the RD3 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000001.10, covering RD3 transcript NM_001164688.1.

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

 (upstream sequence)
                                         .         .                g.5021
                                        ttcatgcccattacagtattc       c.-1141

 .         .         .         .         .         .                g.5081
 ccatgcccctcacagggcagtgtgcatctgttttagtgctacctaatgtctgttaggtgc       c.-1081

 .         .         .         .         .         .                g.5141
 aagctggcccacacatggcttctaggcagaacagtctacaagtgacagcgtgaccagaga       c.-1021

 .         .         .         .         .         .                g.5201
 gcagagacaggaaggaggcccagacatgagtgtgggatgctgcagaacagcaacaggatg       c.-961

 .         .         .         .         .         .                g.5261
 cttctgctatccccaaatgttatctcaaatacctcaacgtcaatgctttctgttccatgt       c.-901

 .         .         .         .         .         .                g.5321
 tcctcttctccctggacagcccctccttctgaaagtcagaactgtctgctcttgagcttg       c.-841

 .         .         .         .         .         .                g.5381
 ccttgagggaaggaaataatttagataagcagagaggaagacaggcaagggatgtggtgg       c.-781

 .         .         .         .         .         .                g.5441
 ggcaaaggcggagatgtatcttcacaggtccctgtcctcagcacccagaatcaccccttc       c.-721

 .         .         .         .         .         .                g.5501
 cctgtaggagggagctgatagaaagaggggatctccatccaggagccacccaccaggcag       c.-661

 .         .         .         .         .         .                g.5561
 ctggaaacatttgccaacagcaggtacacctagggctcagcagagggttgggtgagaatg       c.-601

 .         .         .         .         .         .                g.5621
 gtcttgcccagtttgtgccacactgagcaccggctggaggaggaagcggacagaatgcca       c.-541

 .         .         .         .         .         .                g.5681
 tctggacacaagtgctccctcactgcctgggcctgggtcgcctcaggcttttgtgtcaga       c.-481

 .         .         .         .         .         .                g.5741
 tcagccactccctctacagataatgctgctccaggcaaagaggcttaggtgggtctccag       c.-421

 .         .         .         .         .         .                g.5801
 ggcaaccgcagctcaggagctggcccgcctccatggttcatcagggaagctgtggctcca       c.-361

 .         .         .         .         .         .                g.5861
 gcctcgcgggatacatacacgcatacacacacacacacacacacacacacacacacacac       c.-301

 .         .         .         .         .         .                g.5921
 acacacacctacacaccccacaaacaatagtccaggctggatctctcctcctgtctcttc       c.-241

 .         .         .         .         .         .                g.5981
 tcttggtaaaacttctcagagaaccaaagagaggcaaaatttgaggccagccggcagcag       c.-181

 .         .         .         .         .         .                g.6041
 cagagaagctgagggagacttgaggatgtagactgccctgccctgctgtggctgctcaac       c.-121

 .         .         .         .         .         .                g.6101
 tttctttttttttcctgaaaatatccagacactctcttctcccagactgggaagcagaac       c.-61

 .         .         .         .         .         | 02             g.16502
 gcaggccccctgctgtgacgctgcacctgagcagaggctgacctcagag | ggccaggggct    c.-1

          .         .         .         .         .         .       g.16562
 ATGTCTCTCATCTCATGGCTTCGGTGGAACGAGGCCCCATCCCGGCTGTCCACCAGGAGC       c.60
 M  S  L  I  S  W  L  R  W  N  E  A  P  S  R  L  S  T  R  S         p.20

          .         .         .         .         .         .       g.16622
 CCTGCTGAGATGGTGCTGGAGACGCTTATGATGGAGCTGACGGGGCAGATGCGAGAGGCT       c.120
 P  A  E  M  V  L  E  T  L  M  M  E  L  T  G  Q  M  R  E  A         p.40

          .         .         .         .         .         .       g.16682
 GAGAGGCAGCAGCGGGAGCGCAGCAATGCGGTCAGAAAGGTCTGCACCGGTGTGGACTAC       c.180
 E  R  Q  Q  R  E  R  S  N  A  V  R  K  V  C  T  G  V  D  Y         p.60

          .         .         .         .         .         .       g.16742
 AGCTGGCTGGCCAGCACACCCCGGTCCACCTATGACCTCAGCCCCATTGAGCGGTTGCAG       c.240
 S  W  L  A  S  T  P  R  S  T  Y  D  L  S  P  I  E  R  L  Q         p.80

          .         .         .         .         .       | 03 .    g.18594
 CTGGAAGATGTCTGCGTTAAGATCCACCCATCCTATTGTGGGCCTGCTATCCTCAG | GTTC    c.300
 L  E  D  V  C  V  K  I  H  P  S  Y  C  G  P  A  I  L  R  |  F      p.100

          .         .         .         .         .         .       g.18654
 CGGCAGCTGCTGGCGGAGCAGGAGCCCGAGGTGCAGGAGGTGTCCCAGCTCTTCCGCTCG       c.360
 R  Q  L  L  A  E  Q  E  P  E  V  Q  E  V  S  Q  L  F  R  S         p.120

          .         .         .         .         .         .       g.18714
 GTGCTGCAGGAGGTCCTGGAGAGGATGAAGCAGGAAGAGGAGGCCCACAAGCTGACGCGC       c.420
 V  L  Q  E  V  L  E  R  M  K  Q  E  E  E  A  H  K  L  T  R         p.140

          .         .         .         .         .         .       g.18774
 CAGTGGAGCCTGCGGCCCCGCGGCAGCCTGGCCACCTTCAAGACCCGCGCGCGCATCTCG       c.480
 Q  W  S  L  R  P  R  G  S  L  A  T  F  K  T  R  A  R  I  S         p.160

          .         .         .         .         .         .       g.18834
 CCCTTCGCCAGCGACATCAGGACCATCTCCGAGGACGTGGAGCGGGACACACCGCCGCCA       c.540
 P  F  A  S  D  I  R  T  I  S  E  D  V  E  R  D  T  P  P  P         p.180

          .         .         .         .                           g.18882
 CTGCGGTCCTGGAGCATGCCCGAATTCCGGGCGCCCAAAGCCGACTGA                   c.588
 L  R  S  W  S  M  P  E  F  R  A  P  K  A  D  X                     p.195

          .         .         .         .         .         .       g.18942
 ccccggccgcttccctgcccagaagcggagccttctgcagggggaatgataggccggtga       c.*60

          .         .         .         .         .         .       g.19002
 ccggagcgccgggccctggaacctccccacctaggcctgacgaggagacccaagaggcgg       c.*120

          .         .         .         .         .         .       g.19062
 ccccatcccaagacgctgctataaaatgaagcgactccctgccccatcctcttcctctgg       c.*180

          .         .         .         .         .         .       g.19122
 ccacaaagctgagttaggtcgtagagcggcaccgccctctccctctcctgcgctagtctg       c.*240

          .         .         .         .         .         .       g.19182
 caggagcagccccttccctaactggcagattcaaggttttggaagacagaccattgcccc       c.*300

          .         .         .         .         .         .       g.19242
 atcctcatctcctggttctgtctaaaaggggacagttgccctgccttttggcaagaccta       c.*360

          .         .         .         .         .         .       g.19302
 ggttctcaccccaatttcagggatgtcccattcacccccctacccccatccccaatgaga       c.*420

          .         .         .         .         .         .       g.19362
 agggacctgttggctggtatgccttcttgctagtgactggctgagctcaccactgcaggt       c.*480

          .         .         .         .         .         .       g.19422
 gggtcacacacagcctcataggcaggcacagctggaagggaccagagagacatttagatc       c.*540

          .         .         .         .         .         .       g.19482
 cactctcttcagctagtaaatgtggaacttgaggctcagagagggacacttcttctgcct       c.*600

          .         .         .         .         .         .       g.19542
 ttaactgcagccagctcctcatgaacagtgagattgttcctgcatgaatagtgtctgttc       c.*660

          .         .         .         .         .         .       g.19602
 ctgagtttggaatcctgggctatgaagggacaggtccaaaggctacatctctacctacct       c.*720

          .         .         .         .         .         .       g.19662
 gtggcctgatccatctcttaccttggcagtgggatgagaatctaagctgctctccaagaa       c.*780

          .         .         .         .         .         .       g.19722
 gtgtagctaggggtggaggtaggttactcattaccccacgccacaatgtcatcgcatggg       c.*840

          .         .         .         .         .         .       g.19782
 ctgtggccagtccctaacagcttcttccagaggctcagctccaaggacttcagatgctgc       c.*900

          .         .         .         .         .         .       g.19842
 cctaaagagcccaggtttctcaattccagggttccgctttctgcagctggtcacacctgc       c.*960

          .         .         .         .         .         .       g.19902
 tctctggctttctccagaaagtgatgcccaaacccctgactgaccttgaggcagctgagt       c.*1020

          .         .         .         .         .         .       g.19962
 gaaatgttctagaagagcttcctgcagcttcattgtccttcccttttctaacatggttag       c.*1080

          .         .         .         .         .         .       g.20022
 gccttgatgatgggcatgtggattacccaatgtgtggatcacccatggaaaatctggaag       c.*1140

          .         .         .         .         .         .       g.20082
 gccaggaggccttcccacacactctggggttgaagtggggtgtaagggggatgggtgggg       c.*1200

          .         .         .         .         .         .       g.20142
 aagtgtctaccctcaactaccagcacacatgcagaaaatgcaagtggaccttaatagtag       c.*1260

          .         .         .         .         .         .       g.20202
 cctaaataaaatacccggaggagatataatcaacaggggggaaaagtgtgtattccctca       c.*1320

          .         .         .         .         .         .       g.20262
 gtggaaaaaagtttttttgaatgatttggttttgaacttcccttttgaagtttttttgga       c.*1380

          .         .         .         .         .         .       g.20322
 ttttcacttgaatctggacagagaatcataggatggtggaaaacctctgatccaacacta       c.*1440

          .         .         .         .         .         .       g.20382
 tcaagatgaaagagttgattggcttattaatgtaattggtagaagttgagaatcacttaa       c.*1500

          .         .         .         .         .         .       g.20442
 aatatacatcttaaacatcttacgtattttatttgaagacataaaaagttcacttggttg       c.*1560

          .         .         .         .         .         .       g.20502
 ccaaacttttttttttttttttgagactgagtctcactctgttacccaggctgcagtgca       c.*1620

          .         .         .         .         .         .       g.20562
 gtggcgtgatctcggctcaccacaacctttgcctcccgggttcaagtgattcttctgcct       c.*1680

          .         .         .         .         .         .       g.20622
 cagcctcctaagtagctgggactacaggcacgtgccatcaccccagctaatttttgtatt       c.*1740

          .         .         .         .         .         .       g.20682
 tttattagagatggggtttcactatgttgcccagaatggtcttgaactcctgacctcgtg       c.*1800

          .         .         .         .         .         .       g.20742
 atccactcgccttggcctcccaaagtgctgggattacagacatgagccactgtgcctggc       c.*1860

          .         .         .         .         .         .       g.20802
 tgccaaacttttgatgtgggtccaagctgtgcttttttgtgacctatatgttttgtctgg       c.*1920

          .         .         .         .         .         .       g.20862
 tgggagttctacacttaagttttcttggtttgcactttaatcataacaataagaacaact       c.*1980

          .         .         .         .         .         .       g.20922
 ggcgtaaaagagttttggaacaagcagaagtgacccttggtaagcagactgctcagctgg       c.*2040

          .         .         .         .         .         .       g.20982
 taggggcaaaagtgttgggggaggattagaaaaaggcctccacattgtgggctttccggg       c.*2100

          .         .         .         .         .         .       g.21042
 tgccctggatgtgggtcagcaaatgttttagaggaagtagttaacctggagggagattca       c.*2160

          .         .         .         .         .         .       g.21102
 aaggaggctggataagagaatgtctatttttctccttccctatcaccttacatgtaccta       c.*2220

          .         .         .         .         .         .       g.21162
 ttctccccaaagagaaggaagaccttaggctttcaatgtggtgttctttcttaagtttaa       c.*2280

          .         .         .         .         .         .       g.21222
 gtaactggctgccaatgaaaaccttcccttcgagccgcaggcatgtggacagaatccacc       c.*2340

          .         .         .         .         .         .       g.21282
 accctccttagacactcctcagactactacaggctatccccagctggtggctctcaaatt       c.*2400

          .         .         .         .         .         .       g.21342
 catgagggtccagaagttgttcctctggattcaggttgttaaagggactaatgaggtctg       c.*2460

          .         .         .         .         .                 g.21396
 cttccattactattattgaaacctcaataaccacaaataaaagaacaaaaagtt             c.*2514

 (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 Retinal degeneration 3 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.