cone-rod homeobox (CRX) - coding DNA reference sequence

(used for variant description)

(last modified June 16, 2017)

This file was created to facilitate the description of sequence variants on transcript NM_000554.4 in the CRX gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_008605.1, covering CRX transcript NM_000554.4.

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

 (upstream sequence)
                                         .         .                g.5024
                                     accttggccgggattaccctccga       c.-181

 .         .         .         .         .         .                g.5084
 gttccaggccatgacaaatgacatcactcccggcccaggcttaaaatctccccatgtgag       c.-121

 .         .         .         .         .         .                g.5144
 gggatgtgtttccttcagcctctgctgtctggccgctctgtctaggtcctgggccacggg       c.-61

 .         .         .     | 02   .         .         .             g.17602
 agagccccgtccctcctttctgaag | gccccctgacttgggcctcagtgtccccgaagatc    c.-1

          .         .         .         .         .         .       g.17662
 ATGATGGCGTATATGAACCCGGGGCCCCACTATTCTGTCAACGCCTTGGCCCTAAGTGGC       c.60
 M  M  A  Y  M  N  P  G  P  H  Y  S  V  N  A  L  A  L  S  G         p.20

          .         .         .         . | 03       .         .    g.19421
 CCCAGTGTGGATCTGATGCACCAGGCTGTGCCCTACCCAA | GCGCCCCCAGGAAGCAGCGG    c.120
 P  S  V  D  L  M  H  Q  A  V  P  Y  P  S |   A  P  R  K  Q  R      p.40

          .         .         .         .         .         .       g.19481
 CGGGAGCGCACCACCTTCACCCGGAGCCAACTGGAGGAGCTGGAGGCACTGTTTGCCAAG       c.180
 R  E  R  T  T  F  T  R  S  Q  L  E  E  L  E  A  L  F  A  K         p.60

          .         .         .         .         .         .       g.19541
 ACCCAGTACCCAGACGTCTATGCCCGTGAGGAGGTGGCTCTGAAGATCAATCTGCCTGAG       c.240
 T  Q  Y  P  D  V  Y  A  R  E  E  V  A  L  K  I  N  L  P  E         p.80

          .   | 04     .         .         .         .         .    g.22526
 TCCAGGGTTCAG | GTTTGGTTCAAGAACCGGAGGGCTAAATGCAGGCAGCAGCGACAGCAG    c.300
 S  R  V  Q   | V  W  F  K  N  R  R  A  K  C  R  Q  Q  R  Q  Q      p.100

          .         .         .         .         .         .       g.22586
 CAGAAACAGCAGCAGCAGCCCCCAGGGGGCCAGGCCAAGGCCCGGCCTGCCAAGAGGAAG       c.360
 Q  K  Q  Q  Q  Q  P  P  G  G  Q  A  K  A  R  P  A  K  R  K         p.120

          .         .         .         .         .         .       g.22646
 GCGGGCACGTCCCCAAGACCCTCCACAGATGTGTGTCCAGACCCTCTGGGCATCTCAGAT       c.420
 A  G  T  S  P  R  P  S  T  D  V  C  P  D  P  L  G  I  S  D         p.140

          .         .         .         .         .         .       g.22706
 TCCTACAGTCCCCCTCTGCCCGGCCCCTCAGGCTCCCCAACCACGGCAGTGGCCACTGTG       c.480
 S  Y  S  P  P  L  P  G  P  S  G  S  P  T  T  A  V  A  T  V         p.160

          .         .         .         .         .         .       g.22766
 TCCATCTGGAGCCCAGCCTCAGAGTCCCCTTTGCCTGAGGCGCAGCGGGCTGGGCTGGTG       c.540
 S  I  W  S  P  A  S  E  S  P  L  P  E  A  Q  R  A  G  L  V         p.180

          .         .         .         .         .         .       g.22826
 GCCTCAGGGCCGTCTCTGACCTCCGCCCCCTATGCCATGACCTACGCCCCGGCCTCCGCT       c.600
 A  S  G  P  S  L  T  S  A  P  Y  A  M  T  Y  A  P  A  S  A         p.200

          .         .         .         .         .         .       g.22886
 TTCTGCTCTTCCCCCTCCGCCTATGGGTCTCCGAGCTCCTATTTCAGCGGCCTAGACCCC       c.660
 F  C  S  S  P  S  A  Y  G  S  P  S  S  Y  F  S  G  L  D  P         p.220

          .         .         .         .         .         .       g.22946
 TACCTTTCTCCCATGGTGCCCCAGCTAGGGGGCCCGGCTCTTAGCCCCCTCTCTGGCCCC       c.720
 Y  L  S  P  M  V  P  Q  L  G  G  P  A  L  S  P  L  S  G  P         p.240

          .         .         .         .         .         .       g.23006
 TCCGTGGGACCTTCCCTGGCCCAGTCCCCCACCTCCCTATCAGGCCAGAGCTATGGCGCC       c.780
 S  V  G  P  S  L  A  Q  S  P  T  S  L  S  G  Q  S  Y  G  A         p.260

          .         .         .         .         .         .       g.23066
 TACAGCCCCGTGGATAGCTTGGAATTCAAGGACCCCACGGGCACCTGGAAATTCACCTAC       c.840
 Y  S  P  V  D  S  L  E  F  K  D  P  T  G  T  W  K  F  T  Y         p.280

          .         .         .         .         .         .       g.23126
 AATCCCATGGACCCTCTGGACTACAAGGATCAGAGTGCCTGGAAGTTTCAGATCTTGTAG       c.900
 N  P  M  D  P  L  D  Y  K  D  Q  S  A  W  K  F  Q  I  L  X         p.299

          .         .         .         .         .         .       g.23186
 aggacgcagtctccatctctctccatcgggcctcgggaccctttctcttctgaatctgct       c.*60

          .         .         .         .         .         .       g.23246
 tccctgcagtttagatcccgggatggcattcctgagaaagcaacccgaaccagctgtcct       c.*120

          .         .         .         .         .         .       g.23306
 tctgacagctcggtgttcagcttacagagaccacccctttcctccacagggagaggctcc       c.*180

          .         .         .         .         .         .       g.23366
 tccctctcctgggacagctcacaggtcctagtgattctctcaaccctaacaccgtctggc       c.*240

          .         .         .         .         .         .       g.23426
 acgattgtgaccgctgaagtacaccacgagctccaggcttcagaaagtggtgctgagaac       c.*300

          .         .         .         .         .         .       g.23486
 ttgctccaagaagaagtcaaaccaaacttgcagttgatttggggtcatgtttaggtcaga       c.*360

          .         .         .         .         .         .       g.23546
 atcaccgtgcccttgaacaagcaggtaggggggcttgataacttaactttccacgtggac       c.*420

          .         .         .         .         .         .       g.23606
 agaatttttttttttgttttgtttttgttttgcagacacagtctagctctgtcgcccagg       c.*480

          .         .         .         .         .         .       g.23666
 ctggagtgcagtggcacgatctcagctcactgcaagctctacctcccgggttcacgccat       c.*540

          .         .         .         .         .         .       g.23726
 tctcctgcctcagcctcccgagtagctgggactacagatgcccaccaccaggcccggcta       c.*600

          .         .         .         .         .         .       g.23786
 attttttttgtatttttagtagagacggggtttcaccgtgttagccaggatggtctcgat       c.*660

          .         .         .         .         .         .       g.23846
 ctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggcgtgag       c.*720

          .         .         .         .         .         .       g.23906
 ccaccgcgcccggcccttttttttttttttttttttaattgagacggagtctcactcttt       c.*780

          .         .         .         .         .         .       g.23966
 tgcttaggctggagtgcagtggtgtgatctcagctcactgactgcaacctccacctcccg       c.*840

          .         .         .         .         .         .       g.24026
 ggttgaagcgttgctcctgcctcaatctcccaattagctgggattacaggtgtgctccat       c.*900

          .         .         .         .         .         .       g.24086
 catgcccggctaatttttctattattagtagagacagggttttaccatgttggccaggct       c.*960

          .         .         .         .         .         .       g.24146
 ggtctggaacccctgacctcaagtgatccgcctgcctcggcctcccaaagtgctgggatt       c.*1020

          .         .         .         .         .         .       g.24206
 acaggcatgagccattgtgcctggccctacacgtggacacttctttagcatatggttagg       c.*1080

          .         .         .         .         .         .       g.24266
 gacctttctagaaattccaaagacagactttaagaagccccgtcgggaaaccttaggcca       c.*1140

          .         .         .         .         .         .       g.24326
 atgatgtggttacattaaaaataaattatctgggaatttcacagacttcacaaatgtcag       c.*1200

          .         .         .         .         .         .       g.24386
 gcttacatggtaggtttaggggaccgtttgagagacaaagatctacattcatatatgtag       c.*1260

          .         .         .         .         .         .       g.24446
 ctatacatatatgtactttttcttcttagtttctttttaaagacattttatcactcattc       c.*1320

          .         .         .         .         .         .       g.24506
 gctcattagcacattgggaatgtgtgtatttggtagggaaatgaaaggcaccttgcctgt       c.*1380

          .         .         .         .         .         .       g.24566
 tccatctctactccttttttcttttgttttaggattttctaaaggtgagacactggtgga       c.*1440

          .         .         .         .         .         .       g.24626
 actggggtagctgcttgggacgtaccacctatagttgtggctatttcacagagaagcagc       c.*1500

          .         .         .         .         .         .       g.24686
 agctagacagactcccatctgtaaataaacaagagataggaagagggggaaatagatttg       c.*1560

          .         .         .         .         .         .       g.24746
 gaggaggcagccctacatttcaaacatacattcccttttttagatttttttttttttttt       c.*1620

          .         .         .         .         .         .       g.24806
 tttggttttcagttttgatggtgggattggaaaatagagcttggcttgaggacattttcc       c.*1680

          .         .         .         .         .         .       g.24866
 tggggtggcaccattatttcttgaaatagaatcttacttatggtgacactggcaagcact       c.*1740

          .         .         .         .         .         .       g.24926
 tgtgagaacctgaagacggattgaggtcatttgatgctcagaagttgggtgctgggtccc       c.*1800

          .         .         .         .         .         .       g.24986
 tgccttctcagtccgagttctcctttcatttttgggtggggaggcgggttccaagagccc       c.*1860

          .         .         .         .         .         .       g.25046
 ttcattggtggagttcacaaggcaaggtgtaaaaaaaaaagtagggcaggaagacagtgg       c.*1920

          .         .         .         .         .         .       g.25106
 tgtgctggcagaggtctaacaatgggctctccaaggaagaggaaaaggttggttgtggag       c.*1980

          .         .         .         .         .         .       g.25166
 tgtttgtcagtttccgtggtgtaaatactcccaccacggctgacttcaagctagcaaccg       c.*2040

          .         .         .         .         .         .       g.25226
 gaggtcactgaactaagagttgggaagagatagggcacaatatatgcttacgagttggta       c.*2100

          .         .         .         .         .         .       g.25286
 cacaccgtcagcagcagccagggtcaggagaaaggcgagatgtgaagagaggccgggagg       c.*2160

          .         .         .         .         .         .       g.25346
 tatcagatgacgtttccagcactagaccagaagaggtgcacacagcctagaccccctgag       c.*2220

          .         .         .         .         .         .       g.25406
 gggtacaccctgatctctagagcccacaaagaggtttttattcaacataaaacgtgttca       c.*2280

          .         .         .         .         .         .       g.25466
 tctctcataggcctgagtcatgctgggttctgggacattaagcccaggagtgggccgggt       c.*2340

          .         .         .         .         .         .       g.25526
 gcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcacctga       c.*2400

          .         .         .         .         .         .       g.25586
 ggtcaggagttcgagaccagcctggccaacatggtgaaaccctgtctctactaataatac       c.*2460

          .         .         .         .         .         .       g.25646
 aaaaattagccgggcatggtggcacgcgcctgtaatcccagctactcgggaggctgaggc       c.*2520

          .         .         .         .         .         .       g.25706
 aggagaattgctggaacccgggaggcggaggttgaagagagcagagattgtgccactgtg       c.*2580

          .         .         .         .         .         .       g.25766
 ctctagcctgggtcacaagagcgaaactccgtctcaataataacaacaacaaaaataacc       c.*2640

          .         .         .         .         .         .       g.25826
 caggagtggctcaagagtccagtgtgggatgaaaatataaacagaggaagacaacatatg       c.*2700

          .         .         .         .         .         .       g.25886
 tcactggggaggctgggggagctagacaaaattcacacgggaggggcagggatgagacaa       c.*2760

          .         .         .         .         .         .       g.25946
 tattgtgccctgggtctgtgcaaacgttgggaccagaatccactataagtttcattcttc       c.*2820

          .         .         .         .         .         .       g.26006
 ggagacacggaagctctgcactggaggccgggactcaggcgtggaagagaatcttctcct       c.*2880

          .         .         .         .         .         .       g.26066
 tattcaccggggaggctgtgtcttgtgcaaacaagtcatagaaacttgatgggagttggg       c.*2940

          .         .         .         .         .         .       g.26126
 gagggactgaaggatgcatgcaaggttctgggaaggagtgagaagtagtgaaggccaagg       c.*3000

          .         .         .         .         .         .       g.26186
 ggcccccatcacaggccgatggggtaagacttcgagagagcctgatcctggggtcttctg       c.*3060

          .         .         .         .         .         .       g.26246
 agactccaccaggagccggagagggcagggagccaaatccagctaggaggttacagattg       c.*3120

          .         .         .         .         .         .       g.26306
 cttttcctgggctgggctcctgagtgttggttcttccagctgtgcacaggggatttcaaa       c.*3180

          .         .         .         .         .         .       g.26366
 cgttctacgtcctaaagccaggaagagtgacaaggcaggtggggacagaaggaagaagcc       c.*3240

          .         .         .         .         .         .       g.26426
 aggagcctccctgagaaggtgtcaccttatctgtcctcctcttccccacacactggcctc       c.*3300

          .         .         .         .         .         .       g.26486
 tgggtcccccttctctgtccacccacagagtgaaaccaattaaaatgttggatctcattt       c.*3360

                                                                    g.26489
 aaa                                                                c.*3363

 (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 Cone-rod homeobox 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.