biogenesis of lysosomal organelles complex-1, subunit 6, pallidin (BLOC1S6) - coding DNA reference sequence

(used for variant description)

(last modified July 25, 2014)

This file was created to facilitate the description of sequence variants on transcript NM_012388.2 in the BLOC1S6 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_028194.1, covering BLOC1S6 transcript NM_012388.2.

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

 (upstream sequence)
                     .         .         .         .                g.5045
                acactgcgtccggggccagacgacgatatcagcgcggggtcccca       c.-181

 .         .         .         .         .         .                g.5105
 caacgccatggggcagagccaactctcgagcgcgtgatcgaagcccgcagttttttcgcc       c.-121

 .         .         .         .         .         .                g.5165
 cccgtcacttccgggtgcgacaatctcttctgtccggccagccgctggagtcgttaggtg       c.-61

 .         .         .         .         .         .                g.5225
 ccgccttgcttctgacgagccacacgtttgcttcttccctgtgttcccagctggagggac       c.-1

          .         .         .         .         .         .       g.5285
 ATGAGTGTCCCTGGGCCGTCGTCTCCGGACGGGGCCCTGACACGGCCACCCTACTGCCTG       c.60
 M  S  V  P  G  P  S  S  P  D  G  A  L  T  R  P  P  Y  C  L         p.20

          .         .   | 02     .         .         .         .    g.9954
 GAGGCCGGGGAGCCGACGCCTG | GTTTAAGTGACACTTCTCCAGATGAAGGGTTAATAGAG    c.120
 E  A  G  E  P  T  P  G |   L  S  D  T  S  P  D  E  G  L  I  E      p.40

          .         .         .         .         .         .       g.10014
 GACTTGACTATAGAAGACAAAGCAGTGGAGCAACTGGCAGAAGGATTGCTTTCTCATTAT       c.180
 D  L  T  I  E  D  K  A  V  E  Q  L  A  E  G  L  L  S  H  Y         p.60

          .         .         .         .     | 03   .         .    g.20897
 TTGCCAGATCTGCAGAGATCAAAACAAGCCCTCCAGGAACTCAC | ACAGAACCAAGTTGTA    c.240
 L  P  D  L  Q  R  S  K  Q  A  L  Q  E  L  T  |  Q  N  Q  V  V      p.80

          .         .         .         .         .         .       g.20957
 TTGTTAGACACACTGGAACAAGAGATTTCAAAATTTAAAGAATGTCATTCTATGTTGGAT       c.300
 L  L  D  T  L  E  Q  E  I  S  K  F  K  E  C  H  S  M  L  D         p.100

          .   | 04     .         .         .         .         .    g.23257
 ATTAATGCTTTG | TTTGCTGAGGCTAAACACTATCATGCCAAGTTGGTGAATATAAGAAAA    c.360
 I  N  A  L   | F  A  E  A  K  H  Y  H  A  K  L  V  N  I  R  K      p.120

          .         .         .          | 05        .         .    g.24197
 GAGATGCTGATGCTTCATGAAAAAACATCAAAGTTAAAA | AAAAGAGCACTTAAACTGCAG    c.420
 E  M  L  M  L  H  E  K  T  S  K  L  K   | K  R  A  L  K  L  Q      p.140

          .         .         .         .         .         .       g.24257
 CAGAAGAGGCAAAAAGAAGAGTTGGAAAGGGAGCAGCAACGAGAGAAGGAGTTTGAAAGA       c.480
 Q  K  R  Q  K  E  E  L  E  R  E  Q  Q  R  E  K  E  F  E  R         p.160

          .         .         .                                     g.24296
 GAAAAGCAGTTAACTGCCAGACCAGCCAAAAGGATGTGA                            c.519
 E  K  Q  L  T  A  R  P  A  K  R  M  X                              p.172

          .         .         .         .         .         .       g.24356
 aaagttgtgtttgtgtgttttcttctcctgtcccatatttgggttatgatgactcaagtg       c.*60

          .         .         .         .         .         .       g.24416
 tagactgaagttgaggtagtgccttatgccattatgtcatatgttgaaatccttattccg       c.*120

          .         .         .         .         .         .       g.24476
 gtattactgtgtctccatgccttttttccaagtagcagacgtcatgttgcatggtttttg       c.*180

          .         .         .         .         .         .       g.24536
 atatttatatgtaagtttttcaaattttgcttaattttaaaatttattattttgatcttg       c.*240

          .         .         .         .         .         .       g.24596
 aattatttataaactggaaagtggtttgattattgtgagtcaaaactctaagtggttaaa       c.*300

          .         .         .         .         .         .       g.24656
 aattagtatgaattttttagcttcttaatgaatatggatttaaaactctccagttcttat       c.*360

          .         .         .         .         .         .       g.24716
 tttatgaaatgacttgcctttctggtaatacaatgctgattttttagtaattgccttttc       c.*420

          .         .         .         .         .         .       g.24776
 attactttgttaagaagaaatgccagctgtttaatcacacctacccctggaaaagaggta       c.*480

          .         .         .         .         .         .       g.24836
 aaccttttgaacagttgaatttcatcagaagctctatagctttttggtgagaggaagtga       c.*540

          .         .         .         .         .         .       g.24896
 tactctttattacaagaaacaaggaattaacaaaaataaggaacttgttgctacctttct       c.*600

          .         .         .         .         .         .       g.24956
 tttctgttgaacattaaaaataatttggtttgtggactgggcatggtggcttatggaaaa       c.*660

          .         .         .         .         .         .       g.25016
 gaggtgagcctttgtgaagaacataatggaaaagtgcatgtacgggaaataacagcactt       c.*720

          .         .         .         .         .         .       g.25076
 taggtgtagttcaggtgagcaagatgccagatagtttctactaaccatatactctttctg       c.*780

          .         .         .         .         .         .       g.25136
 cttcttagcgtcgttgtcactgcttctgtggcttttgggttcaaagtagattatatatat       c.*840

          .         .         .         .         .         .       g.25196
 tcctaaagcttggtggaggtagtggagctatcacacactcaaatgagcttgtatatttat       c.*900

          .         .         .         .         .         .       g.25256
 aatacaatatagtattatagtaacagttatcatacactgagatatagtttctgtgcttgt       c.*960

          .         .         .         .         .         .       g.25316
 aaaaaattcttgaagtgaggccgggtgcggtggctcatgcctgtaatcccaacgctttgg       c.*1020

          .         .         .         .         .         .       g.25376
 gacgccgaggcgggtggatcatgaggtcaaaagattgagaccatcctggccaacatggtg       c.*1080

          .         .         .         .         .         .       g.25436
 aaaccccgtctctactagaaatacaaaaattagctgggtgtgggggcgtgcgcctgtagt       c.*1140

          .         .         .         .         .         .       g.25496
 cccagctacttgggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgca       c.*1200

          .         .         .         .         .         .       g.25556
 gtaagccaagatcgtgccactgcactccagccttggtgacagagcaagactccgtctcca       c.*1260

          .         .         .         .         .         .       g.25616
 aaaaaaagaaaaaaaaatttcttgaagtggaatgatgtacaccaaatacccactttatag       c.*1320

          .         .         .         .         .         .       g.25676
 ataattacagggatggtgaaaaattagtaaatagcttcacaaaagaggcagcgtgatacc       c.*1380

          .         .         .         .         .         .       g.25736
 tttagtgttttctagaatttttttctggatattatatgtaagaatttattgtttgaggga       c.*1440

          .         .         .         .         .         .       g.25796
 aatacgaggtttcattgtttaaaatcaagagtgtattgtttactgttttacagtattatt       c.*1500

          .         .         .         .         .         .       g.25856
 taatatccaactggtctccaatctccattacatagggactgtacagagcctgtgaagatg       c.*1560

          .         .         .         .         .         .       g.25916
 tatgaatggtatcttttataatccacaatacatttctggtaagatggaatcactacctct       c.*1620

          .         .         .         .         .         .       g.25976
 gatcacatatcaggctaacgatagagaaagcattaggtttaagttgagggctaagaactg       c.*1680

          .         .         .         .         .         .       g.26036
 gtttgtttaaaggtttaaattgttggaaaagagcatttgccttctttaatgaatgatggt       c.*1740

          .         .         .         .         .         .       g.26096
 ctcacaattcagttgactttgacctaatatttaagaatataaatatattttatttgaaag       c.*1800

          .         .         .         .         .         .       g.26156
 gctgagtgttgccctcaaacacttgctaaaactgcctagggcaggattcattagggcttg       c.*1860

          .         .         .         .         .         .       g.26216
 cagacaatgtcacctaaattgctgaatgtactcattataatatgatatctgacaaaggta       c.*1920

          .         .         .         .         .         .       g.26276
 gtacagcgtttctgagtcatttgggaccaactgcagtggttgtttaaaatgctggttcct       c.*1980

          .         .         .         .         .         .       g.26336
 gcacacaattctctatctactgaagcacatctgttttctttgtttgttttgctttgcttt       c.*2040

          .         .         .         .         .         .       g.26396
 ttgtttttaaagtttcccccagtgattccagtgcacctgaaaagttgagaaccacaggct       c.*2100

          .         .         .         .         .         .       g.26456
 tagtggtacgttggggtttcccacgctaggctgcatagcattataacctgggaacgttaa       c.*2160

          .         .         .         .         .         .       g.26516
 aaaaaatacagacattcttgattcttagtgtagttatgatgtggatcctacgtatttttt       c.*2220

          .         .         .         .         .         .       g.26576
 aaaaaactctccagataattttgatgtcacgagtcactagtatagactatctatctagtg       c.*2280

          .         .         .         .         .         .       g.26636
 agttgtattataagcgatgaaatactttaaaagctacccagtaactcttgggattaattt       c.*2340

          .         .         .         .         .         .       g.26696
 tatgaaataaattctgagctgctgcttttgatatagtcagacttaagactgaaccccagt       c.*2400

          .         .         .         .         .         .       g.26756
 agacaggcaatagatatagaattctggttagctaattgaacttttgtgacctgtttaaaa       c.*2460

          .         .         .         .         .         .       g.26816
 acaaatcaaatttattgaacaaatgacaaggcacaaatactttcagaattgtatttcagt       c.*2520

          .         .         .         .         .         .       g.26876
 tttgaagatttaaaaaaaatgtgaaaataaatatatattagtatcctttattttaaagtc       c.*2580

          .         .         .         .         .         .       g.26936
 aattgtaaaccagaagtactgttattttggtgattaaaatccaaaactttagctgtattt       c.*2640

          .         .         .         .         .         .       g.26996
 cagtaacaaaaacataccttactagactgtgatggctcacacctgtaatcccagtgcttt       c.*2700

          .         .         .         .         .         .       g.27056
 gggaggctgaggtgggaagattctttgagcccaggagttcaaggctgcagtgaattctga       c.*2760

          .         .         .         .         .         .       g.27116
 tcgcaccactgaactccagcccgtatgacagagtgagaccctgtttctaaaaacaaaaca       c.*2820

          .         .         .         .         .         .       g.27176
 aacaaacaaacaaacaacgtatcttactgactaaactggaatggaaatcttataattagt       c.*2880

          .         .         .         .         .         .       g.27236
 gttgtatttttctgcaaaatagtgaattggtacttgggagacttctgttctttgttgaaa       c.*2940

          .         .         .         .         .         .       g.27296
 aaaattgcctttgttttgaaattatatcacctgtgttctgaactaaaatgatgggagttc       c.*3000

          .         .         .         .         .         .       g.27356
 attttgtatttactttgcagtaagtatcatgtaaatatgcaaatgttgaatgtaatatag       c.*3060

          .         .         .         .         .         .       g.27416
 attgtgtcctcattgagtttttgggtgatacagtttataaatataacaattatacaccct       c.*3120

          .         .         .         .         .         .       g.27476
 catacattcgtctgattttgagcttgtaagatgagaactgctttttacacatttaataaa       c.*3180

          .                                                         g.27493
 aaaaggtctctgaatta                                                  c.*3197

 (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 Biogenesis of lysosomal organelles complex-1, subunit 6, pallidin 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.