Hermansky-Pudlak syndrome 5 (HPS5) - 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 HPS5 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000011.9, covering HPS5 transcript NM_181507.1.

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

 (upstream sequence)
          .         .         .         .         .         .       g.60
 CTCTGCCTTTTCTCAGCAATCCTCAGGATATCGCAGGTTCTGGTAAACTTCTCTGACAAC       c.60
 L  C  L  F  S  A  I  L  R  I  S  Q  V  L  V  N  F  S  D  N         p.20

          .         .         .         .         .         .       g.120
 TCAAGGGCCAGACCACATTCCTGTAGCAGTGACCAAGCCCGATCTGGGCCCATGGCCTTA       c.120
 S  R  A  R  P  H  S  C  S  S  D  Q  A  R  S  G  P  M  A  L         p.40

          .         .         .         .         .         .       g.180
 GCTAACAGAAGTGCCACATTCTCCACATTGATGGGGGAAGGCCCATCACTGAGGCTCCCA       c.180
 A  N  R  S  A  T  F  S  T  L  M  G  E  G  P  S  L  R  L  P         p.60

          .         .         .         .         .                 g.231
 TTTAGTGACTCCTGGGGGGCTGGCCTCGTGCTCTTGCTCTGTATGAGATGA                c.231
 F  S  D  S  W  G  A  G  L  V  L  L  L  C  M  R  X                  p.76

          .         .         .         . | 02       .         .    g.1865
 aggagaagcttccattcctccacggtctctgggatccaac | cattgtccccttccatcagg    c.*60

          .         .         .         .         .         .       g.1925
 ctcatatcattcagatacacaatattggtgaaggcctctcttcttctctccagctccaaa       c.*120

          .         .        | 03.         .         .         .    g.3429
 cagagaattagatatccaggccagaaa | ccacaagacctgcagatgtctgtcattttctct    c.*180

          .         .         .         .         .         .       g.3489
 ttggttataaaatctgcaggaagtttaattagatgaaggatcagctgactgtaaccccag       c.*240

          .         .  | 04      .         .         .         .    g.4680
 gaaagcaagtgtgaatgaggc | ctgggataaccttcatcatccattgtgctggtgcttggt    c.*300

          .         .         .         .         .         .       g.4740
 ggagcatcaagggacactgccaaaagcagccaatccaaccttaaagactctggttgcaga       c.*360

          .         .  | 05      .         .         .         .    g.5624
 agggactcaagaaaagatgac | cgctgatcttcaggccttgatttcaccagactgtctaaa    c.*420

          .         .         .         .         .         .       g.5684
 taggccaaaaactcagcaggatgatgatgacaaagttgtatgatatccgatggcaaaatg       c.*480

          .         .         .         .         .        | 06.    g.5946
 gatggaaagaacttgattaaggatcgaagagcagactccccaaacttttcatacaac | cgg    c.*540

          .         .         .         .         .         .       g.6006
 gtagcataaacaaccaacaacggactatcaaaaggaacctcgtcatctagtaactttaac       c.*600

          .         .         .         .         .         | 07    g.9494
 cttgttggtagatctcctttttccatctccatatacacaggattggaacttgccattt | ct    c.*660

          .         .         .         .         .         .       g.9554
 ttcaatccttcaataaaagtatcccaaacagaagggctattactgtaactaagcttgata       c.*720

          .         .         .         .         .         .       g.9614
 ctctccttcgctcttttcaagttcaggagaaaaaagtacttcttcaggaactggcaagcc       c.*780

          .         .         .         .         .         .       g.9674
 agaatttcaggagagtactgttgcaaagtgtggtccacatgtccactggtgcttttgatc       c.*840

          .         .         .         .         .         .       g.9734
 ttagaattcaatacattcaactccaaacataatgttgtcaattcagccaggtcgttccga       c.*900

          .         .         .         .         .         .       g.9794
 agaccacttgcaatggcgcatggagaacatatttgaaacaggtcatccaaagactccctt       c.*960

          .         .         .         .         .         .       g.9854
 ggactccttacacattcacatgctgttttatcaacagattcttcattgcctaaagagtcc       c.*1020

          .         .         .         .         .         .       g.9914
 cttttttctttttcattatcttcatctaatattcccttttttgattcattaactaatagc       c.*1080

          .         .         .         .         .         .       g.9974
 acatcctggttcaatttcatggatgagttgtcagtatctgaaacacctgaaaagtccttc       c.*1140

          .         .         .         .         .         .       g.10034
 atggcaaatgttttttctaaatgtgaaagccactcctgtaaaaccattctcagagactcg       c.*1200

          .         .         .       | 08 .         .         .    g.10973
 gattcaaataaaaccagagggtcctgtagcttggtc | attgcttctgctgttgctacttta    c.*1260

          .         .         .         .         .     | 09   .    g.13076
 agctcctggaacctgtcttcttctggaggtggactagttacctctttttcctcc | tcagtg    c.*1320

          .         .         .         .         .         .       g.13136
 tcttcctcctttgggcaggtatctgaactcacatcctcttcacatgattgctcatcaccc       c.*1380

          .         .         .         .         .         .       g.13196
 ctgagctctggtctcactttcagatcagggctcgtgtgaagggtgccaatcttctcagta       c.*1440

          .         .     | 10   .         .         .         .    g.14085
 gttttacgcacaaagctagaaaca | ctttctttgacagcctgaagagacacaagaggagat    c.*1500

          .         .         .         .         .         .       g.14145
 ggagaacgaaatggtaatggaatgccgaacgggagaaaagtttcattcttatctgtctca       c.*1560

          .         .         | 11         .         .         .    g.14880
 aacatcactggagcatgagaaacattgt | cttcatttccgtgtgagccacaacactgatct    c.*1620

          .         .         .         .         .         .       g.14940
 ggcaggtcctcttcctgctgtgaggtgaattctttaaatctctcatcttctgagagggtt       c.*1680

          .         .         .         .         .         .       g.15000
 tggctgtgaagggagcaagagtcttcatctgactgactgcctcttctactactaatgata       c.*1740

          .         .         .      | 12  .         .         .    g.15634
 cgataaataccagagtccaagatgctgaaactttc | atgtgatgaaatggagcttcttcta    c.*1800

          .         .         .         .         .         .       g.15694
 ctgctacaagctgaatccaaaggttcaaattttaagatcaattcttccagttgagaaatt       c.*1860

          .         .         .         .         .         .       g.15754
 agatcattgtaggtgccatggtccagctgagatttcaaatgctccaatttatctgcagtc       c.*1920

          .     | 13   .         .         .         .         .    g.16888
 aaagtttttcttgc | tctgctggcaatgacagaattttggaaaagacagcatgtacgagca    c.*1980

          .         .         .         .         .         .       g.16948
 gccaagttccataggcctcttcttagcaggcgttccacacagcgctccacagatatcagg       c.*2040

          .         .         .         .         .         .       g.17008
 gagagatgtgagactttcccatttaggtgcaaacagaacaattcattcctacagacagcc       c.*2100

          .    | 14    .         .         .         .         .    g.18925
 acatcctgaatat | ctttgacttcactccaaagaagaacttgaacattctgaggaatgaaa    c.*2160

          .         .         .         .   | 15     .         .    g.23490
 atataaattcctctttctgtccaagtcagcacacaatgctca | ctaagatgtaagagtttg    c.*2220

          .         .         .         .         .     | 16   .    g.24191
 gggaaagacaaagactgggaggatccagctgtatgatcatactgaggttctgat | ctgaga    c.*2280

          .         .         .         .         .         .       g.24251
 gtaatcacagggagaggtggcaacgagaggagtttcttgaactgatgtgtacttataact       c.*2340

          .         .         .         .         .         .       g.24311
 tctccatcaaagttcacttcccacatcctagagcctgggcgagcacaatatatcagaggt       c.*2400

          .         .         .         .         .         .       g.24371
 tgctggcccccagaacatcttccaggaaagaaacaagctccatattctccatctctttcc       c.*2460

          .         .        | 17.         .         .         .    g.27029
 ttgtttccaattttccaaaacttttct | ctctcagtgtcacacaagaaggatcgagtaagt    c.*2520

          .         .         .         .         .         .       g.27089
 gaagatataagtagccttccatccaaataatctaactgtacaacacaggagtcaacagtt       c.*2580

          .         .         .         .  | 18      .         .    g.28810
 gtgattgtctgaacaggaaacatcacaaaagcagcagctgc | ctttgcttgtttagaagta    c.*2640

          .         .         .         .         .         .       g.28870
 ttgagtttgatagcagaaaccttcccagcatgatcacctacaaaaactctaagaatagct       c.*2700

          .         .         .         .         .         .       g.28930
 gtatcccagcagagagctgtgactcttcggcctttgtgttctgaagacacatacatttgt       c.*2760

          .         .         .         .         .     | 19   .    g.29443
 tccggtttcccacgacgctcttgatttaattcccaaacaaccacaagaccttga | ctggta    c.*2820

          .         .         .         .         .          | 20    g.29965
 gctacagcaacataatcatcatcatgtaaacaacaggcgacttgagaaattgcaccttc | c    c.*2880

          .         .         .         .         .         .       g.30025
 ctgtgtgaaagaaaaagcctgtgcttccagccttctttctgaatgagatggagtcctcct       c.*2940

          .         .         .         .         . | 21       .    g.35811
 cctgaactgcccaaagccaaccatttccgagacacagctatgctcgtgca | ctttagacga    c.*3000

          .         .         .         .         .         .       g.35871
 ctggagtccagccgcagggctgagagtaatggatccagagattcaaactctgcaagaaca       c.*3060

          .         .         .         .         .         .       g.35931
 tggctgtaggactctggtatcactggcacaaaagccatttagccagaaagctgaaacttg       c.*3120

          .         .        | 22.         .         .         .    g.40029
 ttgaatgatagatacagtattcctcac | ctttttaacagcagtaactttaatatcttgaga    c.*3180

          .         .         .         .         .         .       g.40089
 tttcttgagaggagacccagtaaccaattttcaaagccaggctcacagaccagcagcccg       c.*3240

          .         .         .         .         .         .       g.40149
 gaggtcccagcccagctccaccacatccagggcagtacctcgcagctctcagtagatcgg       c.*3300

          .         .         .         .         .         .       g.40209
 atcttgtctcccggcttagcgccggggaactcaccgcgcactaagagcggaacgtgaact       c.*3360

          .       | 23 .         .         .         .         .                                               g.40269
 tcagtctcccctcgcg | c                                               c.*3377

 (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 Hermansky-Pudlak syndrome 5 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.