polynucleotide kinase 3'-phosphatase (PNKP) - coding DNA reference sequence

(used for variant description)

(last modified November 16, 2018)

This file was created to facilitate the description of sequence variants on transcript NM_007254.3 in the PNKP gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_027717.1, covering PNKP transcript NM_007254.3.

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

 (upstream sequence)
           .         .         .         .         .                g.5050
           ccgaggaaccgaccgccgccggccgggttgcaggcggggcacctcgggca       c.-61

 .         .         .         .         .       | 02 .             g.5361
 ggacctccctggtcggaagtggccgtgagcccaagccgcggtcccgg | gccggcacccagg    c.-1

          .         .         .         .         .         .       g.5421
 ATGGGCGAGGTGGAGGCCCCGGGCCGCTTGTGGCTCGAGAGCCCCCCTGGGGGAGCGCCC       c.60
 M  G  E  V  E  A  P  G  R  L  W  L  E  S  P  P  G  G  A  P         p.20

          .         .         .         .         .         .       g.5481
 CCCATCTTCCTGCCCTCGGACGGGCAAGCCCTGGTCCTGGGCAGGGGACCCCTGACCCAG       c.120
 P  I  F  L  P  S  D  G  Q  A  L  V  L  G  R  G  P  L  T  Q         p.40

          .         .         .  | 03      .         .         .    g.6149
 GTTACGGACCGGAAGTGCTCCAGAACTCAAG | TGGAGCTGGTCGCAGATCCTGAGACCCGG    c.180
 V  T  D  R  K  C  S  R  T  Q  V |   E  L  V  A  D  P  E  T  R      p.60

          .         | 04         .         .         .         .    g.7181
 ACAGTGGCAGTGAAACAG | CTGGGAGTTAACCCCTCAACTACCGGGACCCAGGAGTTGAAG    c.240
 T  V  A  V  K  Q   | L  G  V  N  P  S  T  T  G  T  Q  E  L  K      p.80

          .         .         .         .         .         .       g.7241
 CCGGGGTTGGAGGGCTCTCTGGGGGTGGGGGACACACTGTATTTGGTCAATGGCCTCCAC       c.300
 P  G  L  E  G  S  L  G  V  G  D  T  L  Y  L  V  N  G  L  H         p.100

          .         .         .         .         .         .       g.7301
 CCACTGACCCTGCGCTGGGAAGAGACCCGCACACCAGAATCCCAGCCAGATACTCCGCCT       c.360
 P  L  T  L  R  W  E  E  T  R  T  P  E  S  Q  P  D  T  P  P         p.120

          .         .         .         .         .         .       g.7361
 GGCACCCCTCTGGTGTCCCAAGATGAGAAGAGAGATGCTGAGCTGCCGAAGAAGCGTATG       c.420
 G  T  P  L  V  S  Q  D  E  K  R  D  A  E  L  P  K  K  R  M         p.140

          .         .         .         .         .         .       g.7421
 CGGAAGTCAAACCCCGGCTGGGAGAACTTGGAGAAGTTGCTAGTGTTCACCGCAGCTGGG       c.480
 R  K  S  N  P  G  W  E  N  L  E  K  L  L  V  F  T  A  A  G         p.160

          .         | 05         .         .         .         .    g.8204
 GTGAAACCCCAGGGCAAG | GTGGCTGGCTTTGATCTGGACGGGACGCTCATCACCACACGC    c.540
 V  K  P  Q  G  K   | V  A  G  F  D  L  D  G  T  L  I  T  T  R      p.180

          .         .         .         | 06         .         .    g.8351
 TCTGGGAAGGTCTTTCCCACTGGCCCCAGTGACTGGAG | GATCTTGTACCCAGAGATTCCC    c.600
 S  G  K  V  F  P  T  G  P  S  D  W  R  |  I  L  Y  P  E  I  P      p.200

          .         .         .       | 07 .         .         .    g.8518
 CGTAAGCTCCGAGAGCTGGAAGCCGAGGGCTACAAG | CTGGTGATCTTCACCAACCAGATG    c.660
 R  K  L  R  E  L  E  A  E  G  Y  K   | L  V  I  F  T  N  Q  M      p.220

          .         .         .         .         .         .       g.8578
 AGCATCGGGCGCGGGAAGCTGCCAGCCGAGGAGTTCAAGGCCAAGGTGGAGGCTGTGGTG       c.720
 S  I  G  R  G  K  L  P  A  E  E  F  K  A  K  V  E  A  V  V         p.240

          .         .     | 08   .         .         .         .    g.8841
 GAGAAGCTGGGGGTCCCCTTCCAG | GTGCTGGTGGCCACGCACGCAGGCTTGTACCGGAAG    c.780
 E  K  L  G  V  P  F  Q   | V  L  V  A  T  H  A  G  L  Y  R  K      p.260

          .         .         .       | 09 .         .         .    g.9851
 CCGGTGACGGGCATGTGGGACCATCTGCAGGAGCAG | GCCAACGACGGCACGCCCATATCC    c.840
 P  V  T  G  M  W  D  H  L  Q  E  Q   | A  N  D  G  T  P  I  S      p.280

          .         .      | 10  .         .         .         .    g.9992
 ATCGGGGACAGCATCTTTGTGGGAG | ACGCAGCCGGACGCCCGGCCAACTGGGCCCCGGGG    c.900
 I  G  D  S  I  F  V  G  D |   A  A  G  R  P  A  N  W  A  P  G      p.300

          .         .         .       | 11 .         .         .    g.10126
 CGGAAGAAGAAAGACTTCTCCTGCGCCGATCGCCTG | TTTGCCCTCAACCTTGGCCTGCCC    c.960
 R  K  K  K  D  F  S  C  A  D  R  L   | F  A  L  N  L  G  L  P      p.320

          .         .         .         .         .         .       g.10186
 TTCGCCACGCCTGAGGAGTTCTTTCTCAAGTGGCCAGCAGCCGGCTTCGAGCTCCCAGCC       c.1020
 F  A  T  P  E  E  F  F  L  K  W  P  A  A  G  F  E  L  P  A         p.340

           | 12        .         .         .         .         .    g.10335
 TTTGATCCG | AGGACTGTCTCCCGCTCAGGGCCTCTCTGCCTCCCCGAGTCCAGGGCCCTC    c.1080
 F  D  P   | R  T  V  S  R  S  G  P  L  C  L  P  E  S  R  A  L      p.360

          .         .         .         .       | 13 .         .    g.10474
 CTGAGCGCCAGCCCGGAGGTGGTTGTCGCAGTGGGATTCCCTGGGG | CCGGGAAGTCCACC    c.1140
 L  S  A  S  P  E  V  V  V  A  V  G  F  P  G  A |   G  K  S  T      p.380

          .         .         .         .         | 14         .    g.10696
 TTTCTCAAGAAGCACCTCGTGTCGGCCGGATATGTCCACGTGAACAGG | GACACGCTAGGC    c.1200
 F  L  K  K  H  L  V  S  A  G  Y  V  H  V  N  R   | D  T  L  G      p.400

          .         .         .         .         .         .       g.10756
 TCCTGGCAGCGCTGTGTGACCACGTGTGAGACAGCCCTGAAGCAAGGGAAACGGGTCGCC       c.1260
 S  W  Q  R  C  V  T  T  C  E  T  A  L  K  Q  G  K  R  V  A         p.420

          .         .         .         | 15         .         .    g.10892
 ATCGACAACACAAACCCAGACGCCGCGAGCCGCGCCAG | GTACGTCCAGTGTGCCCGAGCC    c.1320
 I  D  N  T  N  P  D  A  A  S  R  A  R  |  Y  V  Q  C  A  R  A      p.440

          .         .         .         .         .         .       g.10952
 GCGGGCGTCCCCTGCCGCTGCTTCCTCTTCACCGCCACTCTGGAGCAGGCGCGCCACAAC       c.1380
 A  G  V  P  C  R  C  F  L  F  T  A  T  L  E  Q  A  R  H  N         p.460

        | 16 .         .         .         .         .         .    g.11109
 AACCGG | TTTCGAGAGATGACGGACTCCTCTCATATCCCCGTGTCAGACATGGTCATGTAT    c.1440
 N  R   | F  R  E  M  T  D  S  S  H  I  P  V  S  D  M  V  M  Y      p.480

          | 17         .         .         .         .         .    g.11252
 GGCTACAG | GAAGCAGTTCGAGGCCCCAACGCTGGCTGAAGGCTTCTCTGCCATCCTGGAG    c.1500
 G  Y  R  |  K  Q  F  E  A  P  T  L  A  E  G  F  S  A  I  L  E      p.500

          .         .         .         .         .         .       g.11312
 ATCCCGTTCCGGCTATGGGTGGAGCCGAGGCTGGGGCGGCTGTACTGCCAGTTCTCCGAG       c.1560
 I  P  F  R  L  W  V  E  P  R  L  G  R  L  Y  C  Q  F  S  E         p.520

                                                                    g.11318
 GGCTGA                                                             c.1566
 G  X                                                               p.521

          .         .         .         .                           g.11363
 gccccgcccagctcccctccacaataaacgctgtttctccttgag                      c.*45

 (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 Polynucleotide kinase 3'-phosphatase 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.