partner and localizer of BRCA2 (PALB2) - coding DNA reference sequence

(used for mutation description)

(last modified May 2, 2014)

This file was created to facilitate the description of sequence variants in the PALB2 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000016.9, covering PALB2 transcript NM_024675.3.

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

 (upstream sequence)
          .         .         .         .         .         .       g.60
 CTGCCAGCCTGCCCTGGAGGAAGACAGTACAGCATCACACCCACGCTGAGAGTCGTCTTA       c.60
 L  P  A  C  P  G  G  R  Q  Y  S  I  T  P  T  L  R  V  V  L         p.20

          .         .                                               g.81
 GGGTTAATCACAATGAGCTGA                                              c.81
 G  L  I  T  M  S  X                                                p.26

          .         .         .         .         .         .       g.141
 aacacagggcttcgcaacgactcactctctttggcacagggatgactcaggacaataaag       c.*60

          | 02         .         .         .         .         .    g.6192
 agaagccc | catttcagaataggctttgtgacagactgaagcttggtaagaatcatcaatg    c.*120

          .         .         .       | 03 .         .         .    g.13522
 tgcatctttttcaggagttgaccagtttttaaattc | caaataacaatgttgttcataata    c.*180

          .         .         .         .         .         .       g.13582
 gtagtaccaagcagagcttcttgcatcccttggacctcagcaaaagttagtatagtctcc       c.*240

          .         .         .    | 04    .         .         .    g.15132
 tcagggggcatcaaaaattggttttctttgcct | cctccatcttctgcaaacgtcatgact    c.*300

          .         .         .         .         .         .       g.15192
 tctacttgttgatcagaaagggtcccactgctactaactagcctcctctttgtcaggcca       c.*360

          .         .         .         .         .         .       g.15252
 agcacagcttttatatttccagacttcagtagtacttgcttttcactttcatcatcagag       c.*420

          .      | 05  .         .         .         .         .    g.16190
 gaacaaaacaatgcc | ctgatctctctgatttccaaatttcccaaagctacacacacgaga    c.*480

          .         .         .         .  | 06      .         .    g.18391
 ttatacacatcaggcactggaactatctgtaatactggaac | ctctgcgaagtgccaggta    c.*540

          .         .         .         .         .         .       g.18451
 taaagtttttcccactgccaagcatccagagctttccaaagagaaactacatcttcgcaa       c.*600

          .         .         .         .         .         .       g.18511
 gcagttatgatacatggctctttacaaccggctctttcccaaaacatggcactcacatct       c.*660

          .         .    | 07    .         .         .         .    g.21377
 acggaacaggaacctgaaggatt | ctttaactctgaaaccaattgtaggttgcctgggttt    c.*720

          .         .         .      | 08  .         .         .    g.21801
 atgctatcagaagcaggaagctctgctgtttcagt | ctgttcgacggaatgtttatgcagc    c.*780

          .         .         .         .         .         .       g.21861
 tcctggcatgtgtttctacagagctgattttctttaaaagtgaatgactcaatgggtgga       c.*840

          .         .         .         .         .         .       g.21921
 ggtgttcctggcgggacagagtcacagtcacaggtaggttgtccttgcctgcctgacact       c.*900

          .         .         .         .         .         .       g.21981
 tgcagggtggtatgtggttttgctgggctgcctgaactgtcgaattgtttagtatcactg       c.*960

          .         .         .         .         .         .       g.22041
 gcaagacagactgagtctttcaaatgagcaagttggggtgtgcagcaagttcgtccagca       c.*1020

          .         .         .         .         .         .       g.22101
 acttctgtagatgctttttcataggagccttgagggccaaaggctggagtagtacctaag       c.*1080

          .         .         .         .         .         .       g.22161
 atggggaaagcaggtgaacacatgtctgtggtaggcctgtcattatcatcaggcgcaacc       c.*1140

          .         .         .         .         .         .       g.22221
 gtatttaaaggagtataaagtaatatggatgaagaaaggcccgtctttgtatgctggctt       c.*1200

          .         .         .         .         .         .       g.22281
 tgcgagtttggccttttgggatgtgattttcctggtagaacaataaggtcctcttctaag       c.*1260

          .         .         .         .         .         .       g.22341
 tcctccatttctgtatccatgcgtttaggactcagttcctctggaaaaatacagcttccc       c.*1320

          .         .         .         .         .         .       g.22401
 tctttaagatgtctctctccaaacatttttgactcaaagggctccactggtttttctgag       c.*1380

          .         .         .         .         .         .       g.22461
 caggacttcactttttcaagcttaagaggtccaaagtcttcatcaggtaactgaaagtct       c.*1440

          .         .         .         .         .         .       g.22521
 gtgatactgagaaaagacagtagttgctttaaactcagcattccatccctatgaaatgga       c.*1500

          .         .         .         .         .         .       g.22581
 gccgtgaaagcatcatcatccaaggataaataagcactattactccaagaaagggaatcc       c.*1560

          .         .      | 09  .         .         .         .    g.27033
 tctttttgatgacgacttttcttcc | ctttcacttgaataaataatttttcgtgctgatat    c.*1620

          .         .         .         .         .         .       g.27093
 ttgtgtgaggtgacttcttccttggacctgttaacaatcgacaggctagaagttggcaaa       c.*1680

          .         .         .         .         .         .       g.27153
 agtggttcacaatgatctgatgctggggtgcaggctgattttctttttcctgtgtatctt       c.*1740

          .         .         .         .         .         .       g.27213
 ctaccaggtgcttgggcaactgccttcctagacaagtcattatcttcagtgggcccagcg       c.*1800

          .         .         .         .         .         .       g.27273
 ggagagctgactttagttaatgagagaagtttctgagaggttcttgaacttggttgtcct       c.*1860

          .         .         .         .         .         .       g.27333
 gtgcatgtgccagacatcctaatttcactttggtcagtttcctcattggaaaggtttaaa       c.*1920

          .         .         .         .         .         .       g.27393
 tttttacttgcatccttatttttatttttaaacccttttttcttgacatccaaatgactc       c.*1980

          .         .         .         .         .         .       g.27453
 tgaatgacagcctccacggctactttcctctggcaattggacatgcttcgtgttgttcta       c.*2040

          .         .         .         .         .         .       g.27513
 acataatattctgcaggaaacagaaggccttcaggcactgtgcaagaatgtttttctgca       c.*2100

          .         .         .         .         .         .       g.27573
 gaaagaggagaggttgcttccaggctaagactcttaggttgacttagaatctcactttcc       c.*2160

          .         .         .         .         .         .       g.27633
 tgaagattttcattcctgccatcaagagtgtcactgggagattttaaagatttctctgtt       c.*2220

          .         .         .         .         .         .       g.27693
 tgattttgttcttttaagttttggttttcatttgctggtaagttattgtaggtgagttca       c.*2280

          .         .         .         .         .         .       g.27753
 tttagagaacatgaaatatttgcctctaaattagaacttgtgggcagttggccactttta       c.*2340

          .         .         .         .         .         .       g.27813
 cttatagctttatttacaaggaggttatctgtagagacagtcatttttttgccttgtgcc       c.*2400

          .         .         .         .         .         .       g.27873
 tccaaacttacaggtgaagtaaatctaatgttttttaggtcgtgagtagtaagttcactg       c.*2460

          .         .         .         .         .         .       g.27933
 ctacctttaggaggaatgtgttcaaggtgctgactactaccgctatctgatagagtctgt       c.*2520

          .         .         .         .         .         .       g.27993
 aaaggaactgtagtcgccctggtgaaattaggtcttcttaggaatgtatcaacacctttt       c.*2580

          .         .         .         .         .         .       g.28053
 tctggttgggcagttggtggaattaatacactgtcttcattaatttctgtaactggttct       c.*2640

          .         .         .         .         .         .       g.28113
 ggagaatctggaagttcagatttaagacttaaaaggtgagttcttatttcagttactggt       c.*2700

          .         .         .         .         .         .       g.28173
 gatctagcaggatttttgctactgatttcttcctgttcctttagtcttttcccagacaat       c.*2760

          .         .         .         .         .         .       g.28233
 ctgagtgaatcagtgccaaagacacagtctctctcctgtgaaataaatgtcctcttctgc       c.*2820

          .         .         .         .         .         .       g.28293
 tgcttctttcttctgcttggcagcttctgcttttgctcaccactagggtcactgaccctg       c.*2880

          .         .         .         .         .         .       g.28353
 tggggaaaatgttcttgggtgtcatctgttctttgtataggtaatcctcctgggccatct       c.*2940

          .         .         .         .         .         .       g.28413
 ccagggttaaaggactcaggcccaacatcaagtgtgatagatgtcttttctccagtttct       c.*3000

          .         .         .         .         .         | 10    g.29988
 tcatcaagatgggttttgatgtgtaacttgtcataaacacatattttatttttaggtt | ct    c.*3060

          .         .         .         .         .         .       g.30048
 gagtgttttagctgcggtgagagatcctgctgagacaaacaatcttgttcttctactgtt       c.*3120

          .         .         .         .  | 11      .         .    g.30225
 ttcttaatagaatgcttaatcttttcagctctttgggcacg | ctgaaggcgggctagtgtc    c.*3180

          .         .         .         .  | 12      .         .    g.33265
 ttgctgtattcccttttcaagaatgctaatttctcctttaa | cttttccttctcctcacag    c.*3240

          .         .         .         .         .         .       g.33325
 ctgaggggcttcccgggaggctcgtccatcgggcaggcgacagaacgaaaagagcagccg       c.*3300

          .         .         .         .         .         .       g.33385
 tcgccgaccccaggcctgccgacaccgggacccagttggccctgggccggggaggcgccc       c.*3360

          .         .         .         .         .         .       g.33445
 caggaaggaatggggagcccgggatcgcaccctcagtgcgcgatcagctgacccacgcgg       c.*3420

          .         .         .         .          | 13        .              g.33505
 gccaagcgcgccctaaactccggccaattaaatccaccattcggcctgc | a              c.*3470

 (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 Partner and localizer of BRCA2 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 mutations, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.