copper chaperone for superoxide dismutase (CCS) - coding DNA reference sequence

(used for variant description)

(last modified June 29, 2017)

This file was created to facilitate the description of sequence variants on transcript NM_005125.1 in the CCS gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_008733.1, covering CCS transcript NM_005125.1.

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

 (upstream sequence)
                     .         .         .         .                g.5043
                  cgccggaggagttctgcgtctcggggtggtgactgggtccaga       c.-1

          .         .         .          | 02        .         .    g.5444
 ATGGCTTCGGATTCGGGGAACCAGGGGACCCTCTGCACG | TTGGAGTTCGCGGTGCAGATG    c.60
 M  A  S  D  S  G  N  Q  G  T  L  C  T   | L  E  F  A  V  Q  M      p.20

          .         .         .         .         .   | 03     .    g.10905
 ACCTGTCAGAGCTGTGTGGACGCGGTGCGCAAATCCCTGCAAGGGGTGGCAG | GTGTCCAG    c.120
 T  C  Q  S  C  V  D  A  V  R  K  S  L  Q  G  V  A  G |   V  Q      p.40

          .         .         .         .         .         .       g.10965
 GATGTGGAGGTGCACTTGGAGGACCAGATGGTCTTGGTACACACCACTCTACCCAGCCAG       c.180
 D  V  E  V  H  L  E  D  Q  M  V  L  V  H  T  T  L  P  S  Q         p.60

          .         .         .         .         .         .       g.11025
 GAGGTGCAGGCTCTCCTGGAAGGCACGGGGCGGCAGGCGGTACTCAAGGGCATGGGCAGC       c.240
 E  V  Q  A  L  L  E  G  T  G  R  Q  A  V  L  K  G  M  G  S         p.80

          . | 04       .         .         .         .         .    g.11290
 GGCCAGTTGC | AGAATCTGGGGGCAGCAGTGGCCATCCTGGGGGGGCCTGGCACCGTGCAG    c.300
 G  Q  L  Q |   N  L  G  A  A  V  A  I  L  G  G  P  G  T  V  Q      p.100

          .         .         .         .         .         .       g.11350
 GGGGTGGTGCGCTTCCTACAGCTGACCCCTGAGCGCTGCCTCATCGAGGGAACTATTGAC       c.360
 G  V  V  R  F  L  Q  L  T  P  E  R  C  L  I  E  G  T  I  D         p.120

          .         .         .         .         .         .       g.11410
 GGCCTGGAGCCTGGGCTGCATGGACTCCACGTCCATCAGTACGGGGACCTTACAAACAAC       c.420
 G  L  E  P  G  L  H  G  L  H  V  H  Q  Y  G  D  L  T  N  N         p.140

          | 05         .         .         .         .         .    g.12322
 TGCAACAG | CTGTGGGAATCACTTTAACCCTGATGGAGCATCTCATGGGGGCCCCCAGGAC    c.480
 C  N  S  |  C  G  N  H  F  N  P  D  G  A  S  H  G  G  P  Q  D      p.160

           | 06        .         .         .         .         .    g.17171
 TCTGACCGG | CACCGCGGAGACCTGGGCAATGTCCGTGCTGATGCTGACGGCCGCGCCATC    c.540
 S  D  R   | H  R  G  D  L  G  N  V  R  A  D  A  D  G  R  A  I      p.180

          .         .        | 07.         .         .         .    g.17303
 TTCAGAATGGAGGATGAGCAGCTGAAG | GTGTGGGATGTGATTGGCCGCAGCCTGATTATT    c.600
 F  R  M  E  D  E  Q  L  K   | V  W  D  V  I  G  R  S  L  I  I      p.200

          .         .         .         .         .         .       g.17363
 GATGAGGGAGAAGATGACCTGGGCCGGGGAGGCCATCCCTTATCCAAGATCACAGGGAAC       c.660
 D  E  G  E  D  D  L  G  R  G  G  H  P  L  S  K  I  T  G  N         p.220

          .  | 08      .         .         .         .         .    g.17532
 TCCGGGGAGAG | GTTGGCCTGTGGCATCATTGCACGCTCCGCTGGCCTTTTCCAGAACCCC    c.720
 S  G  E  R  |  L  A  C  G  I  I  A  R  S  A  G  L  F  Q  N  P      p.240

          .         .         .         .         .         .       g.17592
 AAGCAGATCTGCTCTTGCGATGGCCTCACCATCTGGGAGGAGCGAGGCCGGCCCATCGCT       c.780
 K  Q  I  C  S  C  D  G  L  T  I  W  E  E  R  G  R  P  I  A         p.260

          .         .         .         .                           g.17637
 GGCAAGGGCCGAAAGGAGTCAGCGCAGCCCCCTGCCCACCTTTGA                      c.825
 G  K  G  R  K  E  S  A  Q  P  P  A  H  L  X                        p.274

          .         .         .         .         .         .       g.17697
 gcaggacctcaccttggctctgttgctgtcctccagggcgagcactttccacttccagag       c.*60

          .         .         .         .         .         .       g.17757
 ggggccagagggactttgcctgcccagtctttggagagctcagtacagggcaggagctgc       c.*120

          .         .         .         .                           g.17801
 tgtggtgttcccttggcaaatgaaagttttattttcgtttggga                       c.*164

 (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 Copper chaperone for superoxide dismutase 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.