cholinergic receptor, nicotinic, alpha 1 (muscle) (CHRNA1) - coding DNA reference sequence

(used for mutation description)

(last modified February 12, 2011)


This file was created to facilitate the description of sequence variants in the CHRNA1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008172.1, covering CHRNA1 transcript-1 (NM_001039523.2). Transcript variant-2 lacks the alternatively spliced exon 4 (NM_000079.3). The protein is N-terminally cleaved to obtain the mature CHRNA1 protein, removing the signal peptide (amino acids 1-20). Publications describing variants in CHRNA1 originally used the mature protein as a reference (also excl. the 25 amino acids encoded by exon 4). 

Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                                                   .                g.5018
                                           agacaagcacccagccag       c.-61

 .         .         .         .         .         .                g.5078
 agtgccagtgagaagcacaggccaccactctgccctggtccacacaagctccggtagccc       c.-1

          .         .         .         .    | 02    .         .    g.9856
 ATGGAGCCCTGGCCTCTCCTCCTGCTCTTTAGCCTTTGCTCAG | CTGGCCTCGTCCTGGGC    c.60
 M  E  P  W  P  L  L  L  L  F  S  L  C  S  A |   G  L  V  L  G      p.20

          .         .         .         .         .         .       g.9916
 TCCGAACATGAGACCCGTCTGGTGGCAAAGCTATTTAAAGACTACAGCAGCGTGGTGCGG       c.120
 S  E  H  E  T  R  L  V  A  K  L  F  K  D  Y  S  S  V  V  R         p.40

          .         .         .         .         .         .       g.9976
 CCAGTGGAAGACCACCGCCAGGTCGTGGAGGTCACCGTGGGCCTGCAGCTGATACAGCTC       c.180
 P  V  E  D  H  R  Q  V  V  E  V  T  V  G  L  Q  L  I  Q  L         p.60

           | 03        .         .         .         .     | 04   . g.11458
 ATCAATGTG | GATGAAGTAAATCAGATCGTGACAACCAATGTGCGTCTGAAACAG | GGTGAC c.240
 I  N  V   | D  E  V  N  Q  I  V  T  T  N  V  R  L  K  Q   | G  D   p.80
                                                           ^  alternatively spliced exon

          .         .         .         .         .         .       g.11518
 ATGGTAGATCTGCCACGCCCCAGCTGCGTGACTTTGGGAGTTCCTTTGTTTTCTCATCTG       c.300
 M  V  D  L  P  R  P  S  C  V  T  L  G  V  P  L  F  S  H  L         p.100

           | 05        .         .         .         .         .    g.11848
 CAGAATGAG | CAATGGGTGGATTACAACCTAAAATGGAATCCAGATGACTATGGCGGTGTG    c.360
 Q  N  E   | Q  W  V  D  Y  N  L  K  W  N  P  D  D  Y  G  G  V      p.120

          .         .         .         .         .          | 06    g.15059
 AAAAAAATTCACATTCCTTCAGAAAAGATCTGGCGCCCAGACCTTGTTCTCTATAACAA | T    c.420
 K  K  I  H  I  P  S  E  K  I  W  R  P  D  L  V  L  Y  N  N  |      p.140

          .         .         .         .         .         .       g.15119
 GCAGATGGTGACTTTGCTATTGTCAAGTTCACCAAAGTGCTCCTGCAGTACACTGGCCAC       c.480
 A  D  G  D  F  A  I  V  K  F  T  K  V  L  L  Q  Y  T  G  H         p.160

          .         .         .         .         .         .       g.15179
 ATCACGTGGACACCTCCAGCCATCTTTAAAAGCTACTGTGAGATCATCGTCACCCACTTT       c.540
 I  T  W  T  P  P  A  I  F  K  S  Y  C  E  I  I  V  T  H  F         p.180

          .         .         .         .         .         .       g.15239
 CCCTTTGATGAACAGAACTGCAGCATGAAGCTGGGCACCTGGACCTACGACGGCTCTGTC       c.600
 P  F  D  E  Q  N  C  S  M  K  L  G  T  W  T  Y  D  G  S  V         p.200

          .      | 07  .         .         .         .         .    g.15777
 GTGGCCATCAACCCG | GAAAGCGACCAGCCAGACCTGAGCAACTTCATGGAGAGCGGGGAG    c.660
 V  A  I  N  P   | E  S  D  Q  P  D  L  S  N  F  M  E  S  G  E      p.220

          .         .         .         .         .         .       g.15837
 TGGGTGATCAAGGAGTCCCGGGGCTGGAAGCACTCCGTGACCTATTCCTGCTGCCCCGAC       c.720
 W  V  I  K  E  S  R  G  W  K  H  S  V  T  Y  S  C  C  P  D         p.240

          .         .         .         .         .         .       g.15897
 ACCCCCTACCTGGACATCACCTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATC       c.780
 T  P  Y  L  D  I  T  Y  H  F  V  M  Q  R  L  P  L  Y  F  I         p.260

          .         .         .         .         .         .       g.15957
 GTCAACGTCATCATCCCCTGCCTGCTCTTCTCCTTCTTAACTGGCCTGGTATTCTACCTG       c.840
 V  N  V  I  I  P  C  L  L  F  S  F  L  T  G  L  V  F  Y  L         p.280

          .    | 08    .         .         .         .         .    g.19350
 CCCACAGACTCAG | GGGAGAAGATGACTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTG    c.900
 P  T  D  S  G |   E  K  M  T  L  S  I  S  V  L  L  S  L  T  V      p.300

          .         .         .         .         .         .       g.19410
 TTCCTTCTGGTCATCGTGGAGCTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGA       c.960
 F  L  L  V  I  V  E  L  I  P  S  T  S  S  A  V  P  L  I  G         p.320

          .         .         .         .         .         .       g.19470
 AAATACATGCTGTTCACCATGGTGTTCGTCATTGCCTCCATCATCATCACTGTCATCGTC       c.1020
 K  Y  M  L  F  T  M  V  F  V  I  A  S  I  I  I  T  V  I  V         p.340

          .         .         .         .         .        | 09.    g.20656
 ATCAACACACACCACCGCTCACCCAGCACCCATGTCATGCCCAACTGGGTGCGGAAG | GTT    c.1080
 I  N  T  H  H  R  S  P  S  T  H  V  M  P  N  W  V  R  K   | V      p.360

          .         .         .         .         .         .       g.20716
 TTTATCGACACTATCCCAAATATCATGTTTTTCTCCACAATGAAAAGACCATCCAGAGAA       c.1140
 F  I  D  T  I  P  N  I  M  F  F  S  T  M  K  R  P  S  R  E         p.380

          .         .         .         .         .         .       g.20776
 AAGCAAGACAAAAAGATTTTTACAGAAGACATTGATATCTCTGACATTTCTGGAAAGCCA       c.1200
 K  Q  D  K  K  I  F  T  E  D  I  D  I  S  D  I  S  G  K  P         p.400

          .         .         .         .         .         .       g.20836
 GGGCCTCCACCCATGGGCTTCCACTCTCCCCTGATCAAACACCCCGAGGTGAAAAGTGCC       c.1260
 G  P  P  P  M  G  F  H  S  P  L  I  K  H  P  E  V  K  S  A         p.420

          .         .         .         .         .        | 10.    g.21220
 ATCGAGGGCATCAAGTACATCGCAGAGACCATGAAGTCAGACCAGGAGTCTAACAAT | GCG    c.1320
 I  E  G  I  K  Y  I  A  E  T  M  K  S  D  Q  E  S  N  N   | A      p.440

          .         .         .         .         .         .       g.21280
 GCGGCAGAGTGGAAGTACGTTGCAATGGTGATGGACCACATACTCCTCGGAGTCTTCATG       c.1380
 A  A  E  W  K  Y  V  A  M  V  M  D  H  I  L  L  G  V  F  M         p.460

          .         .         .         .         .         .       g.21340
 CTTGTTTGCATCATCGGAACCCTAGCCGTGTTTGCAGGTCGACTCATTGAATTAAATCAG       c.1440
 L  V  C  I  I  G  T  L  A  V  F  A  G  R  L  I  E  L  N  Q         p.480

                                                                    g.21349
 CAAGGATGA                                                          c.1449
 Q  G  X                                                            p.482

          .         .         .         .         .         .       g.21409
 gcagaaaatgagctgagcttagctctgccctggaacctaccagagcagagaagggcagga       c.*60

          .         .         .         .         .         .       g.21469
 gaggaagatttgtctacttgctccactcgcacttatcaaacgtgttatattccatactta       c.*120

          .         .         .         .         .         .       g.21529
 ttattgatgataagatttacctttatgtaagtttatggccttgaagtgttttcatattgc       c.*180

          .         .         .         .         .         .       g.21589
 ttctccctttagttctgctgtctccctgaagagtgaaccctctttagtaaatgaaactaa       c.*240

          .         .         .         .         .         .       g.21649
 tcactaaaaaaagtgttcatttccagtgtctggaagagtttttgccaggataaccgaggt       c.*300

          .         .         .         .         .         .       g.21709
 tttctgttgcattgtcattgctgttatatttatatatttacttattttgtctaaccacga       c.*360

          .         .         .         .         .         .       g.21769
 gaccactagggagttgctgatgttctaaatgaagtgtattctttgcttaagagtcagttt       c.*420

          .         .         .         .         .         .       g.21829
 tgtacctactaagaaaaccccatctaccagtcctaaagagataaggcatttgatttggag       c.*480

          .         .         .         .         .                 g.21881
 agagaggaagcagtagaaatgaaataaactaaaatgcaaactgcatcaaaaa               c.*532

 (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 10th nucleotide is indicated by a "." above the sequence. The Cholinergic receptor, nicotinic, alpha 1 (muscle) protein sequence is shown below the coding DNA sequence, with numbering indicated at the right starting with 1 for the translation initiating Methionine. Every 10th 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.

Powered by LOVD v.2.0 Build 29
©2004-2011 Leiden University Medical Center