calpain 3, (p94) (CAPN3) - coding DNA reference sequence

(used for variant description)

(last modified January 20, 2019)


This file was created to facilitate the description of sequence variants on transcript NM_000070.2 in the CAPN3 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008660.1, covering CAPN3 transcript NM_000070.2. Several differentially spliced CAPN3-transcripts have been described; variant-2 (NM_024344.1) lacking exon 15 and variant-3 (NM_173087.1) lacking exons 6, 15 and 16. Transcript variant-7 (NM_212465.2) uses an upstream promoter/first exon 01b and 5 exons replacing the normal exon 1 and lacks exon 15. Other transcripts use an alterantive promoter/first-exon in intron 12 (variant-4, NM_173088.1) or intron 14 (variant-6 lacking exon 16, NM_173090.1) and variant-5 (lacking exons 15 and 16, NM_173089.1).

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


 (upstream sequence)
           ^  alternative promoter/first exon 01b                                                                    g.16403
                                                       cactct       c.-301

 .         .         .         .         .         .                g.16463
 ctttctctctccctctggcatgcatgctgctggtaggagacccccaagtcaacattgctt       c.-241

 .         .         .         .         .         .                g.16523
 cagaaatcctttagcactcatttctcaggagaacttatggcttcagaatcacagctcggt       c.-181

 .         .         .         .         .         .                g.16583
 ttttaagatggacataacctgtacgaccttctgatgggctttcaactttgaactggatgt       c.-121

 .         .         .         .         .         .                g.16643
 ggacacttttctctcagatgacagaattactccaacttcccctttgcagttgcttccttt       c.-61

 .         .         .         .         .         .                g.16703
 ccttgaaggtagctgtatcttattttctttaaaaagctttttcttccaaagccacttgcc       c.-1

          .         .         .         .         .         .       g.16763
 ATGCCGACCGTCATTAGCGCATCTGTGGCTCCAAGGACAGCGGCTGAGCCCCGGTCCCCA       c.60
 M  P  T  V  I  S  A  S  V  A  P  R  T  A  A  E  P  R  S  P         p.20

          .         .         .         .         .         .       g.16823
 GGGCCAGTTCCTCACCCGGCCCAGAGCAAGGCCACTGAGGCTGGGGGTGGAAACCCAAGT       c.120
 G  P  V  P  H  P  A  Q  S  K  A  T  E  A  G  G  G  N  P  S         p.40

          .         .         .         .         .         .       g.16883
 GGCATCTATTCAGCCATCATCAGCCGCAATTTTCCTATTATCGGAGTGAAAGAGAAGACA       c.180
 G  I  Y  S  A  I  I  S  R  N  F  P  I  I  G  V  K  E  K  T         p.60

          .         .         .         .         .         .       g.16943
 TTCGAGCAACTTCACAAGAAATGTCTAGAAAAGAAAGTTCTTTATGTGGACCCTGAGTTC       c.240
 F  E  Q  L  H  K  K  C  L  E  K  K  V  L  Y  V  D  P  E  F         p.80

          .         .         .         .         .         .       g.17003
 CCACCGGATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCATCCAGTTCGTCTGGAAG       c.300
 P  P  D  E  T  S  L  F  Y  S  Q  K  F  P  I  Q  F  V  W  K         p.100

           | 02        .         .         .         .         .    g.41431
 AGACCTCCG | GAAATTTGCGAGAATCCCCGATTTATCATTGATGGAGCCAACAGAACTGAC    c.360
 R  P  P   | E  I  C  E  N  P  R  F  I  I  D  G  A  N  R  T  D      p.120

          .          | 03        .         .         .         .    g.43105
 ATCTGTCAAGGAGAGCTAG | GGGACTGCTGGTTTCTCGCAGCCATTGCCTGCCTGACCCTG    c.420
 I  C  Q  G  E  L  G |   D  C  W  F  L  A  A  I  A  C  L  T  L      p.140

          .         .         .         .         .         .       g.43165
 AACCAGCACCTTCTTTTCCGAGTCATACCCCATGATCAAAGTTTCATCGAAAACTACGCA       c.480
 N  Q  H  L  L  F  R  V  I  P  H  D  Q  S  F  I  E  N  Y  A         p.160

          .         | 04         .         .         .         .    g.44692
 GGGATCTTCCACTTCCAG | TTCTGGCGCTATGGAGAGTGGGTGGACGTGGTTATAGATGAC    c.540
 G  I  F  H  F  Q   | F  W  R  Y  G  E  W  V  D  V  V  I  D  D      p.180

          .         .         .         .         .         .       g.44752
 TGCCTGCCAACGTACAACAATCAACTGGTTTTCACCAAGTCCAACCACCGCAATGAGTTC       c.600
 C  L  P  T  Y  N  N  Q  L  V  F  T  K  S  N  H  R  N  E  F         p.200

          .         .         .   | 05     .         .         .    g.45853
 TGGAGTGCTCTGCTGGAGAAGGCTTATGCTAA | GCTCCATGGTTCCTACGAAGCTCTGAAA    c.660
 W  S  A  L  L  E  K  A  Y  A  K  |  L  H  G  S  Y  E  A  L  K      p.220

          .         .         .         .         .         .       g.45913
 GGTGGGAACACCACAGAGGCCATGGAGGACTTCACAGGAGGGGTGGCAGAGTTTTTTGAG       c.720
 G  G  N  T  T  E  A  M  E  D  F  T  G  G  V  A  E  F  F  E         p.240

          .         .         .         .         .         .       g.45973
 ATCAGGGATGCTCCTAGTGACATGTACAAGATCATGAAGAAAGCCATCGAGAGAGGCTCC       c.780
 I  R  D  A  P  S  D  M  Y  K  I  M  K  K  A  I  E  R  G  S         p.260

          .         .  | 06      .         .         .         .    g.46889
 CTCATGGGCTGCTCCATTGAT | GATGGCACGAACATGACCTATGGAACCTCTCCTTCTGGT    c.840
 L  M  G  C  S  I  D   | D  G  T  N  M  T  Y  G  T  S  P  S  G      p.280

          .         .         .         .         .         .       g.46949
 CTGAACATGGGGGAGTTGATTGCACGGATGGTAAGGAATATGGATAACTCACTGCTCCAG       c.900
 L  N  M  G  E  L  I  A  R  M  V  R  N  M  D  N  S  L  L  Q         p.300

          .         .         .         .      | 07  .         .    g.49551
 GACTCAGACCTCGACCCCAGAGGCTCAGATGAAAGACCGACCCGG | ACAATCATTCCGGTT    c.960
 D  S  D  L  D  P  R  G  S  D  E  R  P  T  R   | T  I  I  P  V      p.320

          .         .         .         .         .         .       g.49611
 CAGTATGAGACAAGAATGGCCTGCGGGCTGGTCAGAGGTCACGCCTACTCTGTCACGGGG       c.1020
 Q  Y  E  T  R  M  A  C  G  L  V  R  G  H  A  Y  S  V  T  G         p.340

           | 08        .         .         .         .         .    g.51204
 CTGGATGAG | GTCCCGTTCAAAGGTGAGAAAGTGAAGCTGGTGCGGCTGCGGAATCCGTGG    c.1080
 L  D  E   | V  P  F  K  G  E  K  V  K  L  V  R  L  R  N  P  W      p.360

          .         .         .      | 09  .         .         .    g.53722
 GGCCAGGTGGAGTGGAACGGTTCTTGGAGTGATAG | ATGGAAGGACTGGAGCTTTGTGGAC    c.1140
 G  Q  V  E  W  N  G  S  W  S  D  R  |  W  K  D  W  S  F  V  D      p.380

          .         .         .         .         .    | 10    .    g.56396
 AAAGATGAGAAGGCCCGTCTGCAGCACCAGGTCACTGAGGATGGAGAGTTCTG | GATGTCC    c.1200
 K  D  E  K  A  R  L  Q  H  Q  V  T  E  D  G  E  F  W  |  M  S      p.400

          .         .         .         .         .         .       g.56456
 TATGAGGATTTCATCTACCATTTCACAAAGTTGGAGATCTGCAACCTCACGGCCGATGCT       c.1260
 Y  E  D  F  I  Y  H  F  T  K  L  E  I  C  N  L  T  A  D  A         p.420

          .         .         .         .         .         .       g.56516
 CTGCAGTCTGACAAGCTTCAGACCTGGACAGTGTCTGTGAACGAGGGCCGCTGGGTACGG       c.1320
 L  Q  S  D  K  L  Q  T  W  T  V  S  V  N  E  G  R  W  V  R         p.440

          .         .         .     | 11   .         .         .    g.58564
 GGTTGCTCTGCCGGAGGCTGCCGCAACTTCCCAG | ATACTTTCTGGACCAACCCTCAGTAC    c.1380
 G  C  S  A  G  G  C  R  N  F  P  D |   T  F  W  T  N  P  Q  Y      p.460

          .         .         .         .         .         .       g.58624
 CGTCTGAAGCTCCTGGAGGAGGACGATGACCCTGATGACTCGGAGGTGATTTGCAGCTTC       c.1440
 R  L  K  L  L  E  E  D  D  D  P  D  D  S  E  V  I  C  S  F         p.480

          .         .         .         .         .         .       g.58684
 CTGGTGGCCCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGGCCAGTCTCTTC       c.1500
 L  V  A  L  M  Q  K  N  R  R  K  D  R  K  L  G  A  S  L  F         p.500

          .         .     | 12   .       | 13 .         .         . g.59715
 ACCATTGGCTTCGCCATCTACGAG | GTTCCCAAAGAG | ATGCACGGGAACAAGCAGCACCTG c.1560
 T  I  G  F  A  I  Y  E   | V  P  K  E   | M  H  G  N  K  Q  H  L   p.520
^ alternative promoter/first exon 13b . . . . . . g.59775 CAGAAGGACTTCTTCCTGTACAACGCCTCCAAGGCCAGGAGCAAAACCTACATCAACATG c.1620 Q K D F F L Y N A S K A R S K T Y I N M p.540 . . . . . . g.59835 CGGGAGGTGTCCCAGCGCTTCCGCCTGCCTCCCAGCGAGTACGTCATCGTGCCCTCCACC c.1680 R E V S Q R F R L P P S E Y V I V P S T p.560 . . . . . . g.59895 TACGAGCCCCACCAGGAGGGGGAATTCATCCTCCGGGTCTTCTCTGAAAAGAGGAACCTC c.1740 Y E P H Q E G E F I L R V F S E K R N L p.580 | 14 . . . . | 15 . . g.62841 TCTGA | GGAAGTTGAAAATACCATCTCCGTGGATCGGCCAGTG | AAAAAGAAAAAAACCAAG c.1800 S E | E V E N T I S V D R P V | K K K K T K p.600
^ alternative promoter/first exon 15b | 16 . . . . . . g.65168 | CCCATCATCTTCGTTTCGGACAGAGCAAACAGCAACAAGGAGCTGGGTGTGGACCAGGAG c.1860 | P I I F V S D R A N S N K E L G V D Q E p.620 . . . . . | 17 . g.66206 TCAGAGGAGGGCAAAGGCAAAACAAGCCCTGATAAGCAAAAGCAGTCCCCACAG | CCACAG c.1920 S E E G K G K T S P D K Q K Q S P Q | P Q p.640 . . . . . . g.66266 CCTGGCAGCTCTGATCAGGAAAGTGAGGAACAGCAACAATTCCGGAACATTTTCAAGCAG c.1980 P G S S D Q E S E E Q Q Q F R N I F K Q p.660 . | 18 . . . . . g.66732 ATAGCAGGAGAT | GACATGGAGATCTGTGCAGATGAGCTCAAGAAGGTCCTTAACACAGTC c.2040 I A G D | D M E I C A D E L K K V L N T V p.680 . | 19 . . . . . g.66878 GTGAACAAAC | ACAAGGACCTGAAGACACACGGGTTCACACTGGAGTCCTGCCGTAGCATG c.2100 V N K H | K D L K T H G F T L E S C R S M p.700 . | 20 . . . . . g.67370 ATTGCGCTCATGGAT | ACAGATGGCTCTGGAAAGCTCAACCTGCAGGAGTTCCACCACCTC c.2160 I A L M D | T D G S G K L N L Q E F H H L p.720 . . | 21 . . . . g.67521 TGGAACAAGATTAAGGCCTGGCAG | AAAATTTTCAAACACTATGACACAGACCAGTCCGGC c.2220 W N K I K A W Q | K I F K H Y D T D Q S G p.740 . . . . | 22 . . g.67798 ACCATCAACAGCTACGAGATGCGAAATGCAGTCAACGACGCAG | GATTCCACCTCAACAAC c.2280 T I N S Y E M R N A V N D A G | F H L N N p.760 . . . . . . g.67858 CAGCTCTATGACATCATTACCATGCGGTACGCAGACAAACACATGAACATCGACTTTGAC c.2340 Q L Y D I I T M R Y A D K H M N I D F D p.780 . . . . | 23 . . g.68204 AGTTTCATCTGCTGCTTCGTTAGGCTGGAGGGCATGTTCA | GAGCTTTTCATGCATTTGAC c.2400 S F I C C F V R L E G M F R | A F H A F D p.800 . . . | 24 . . g.68665 AAGGATGGAGATGGTATCATCAAGCTCAACGTTCTGGAG | TGGCTGCAGCTCACCATGTAT c.2460 K D G D G I I K L N V L E | W L Q L T M Y p.820 g.68671 GCCTGA c.2466 A X p.821 . . . . . . g.68731 accaggctggcctcatccaaagccatgcaggatcactcaggatttcagtttcaccctcta c.*60 . . . . . . g.68791 tttccaaagccatttacctcaaaggacccagcagctacacccctacaggcttccaggcac c.*120 . . . . . . g.68851 ctcatcagtcatgctcctcctccattttaccccctacccatccttgatcggtcatgccta c.*180 . . . . . . g.68911 gcctgaccctttagtaaagcaatgaggtaggaagaacaaacccttgtccctttgccatgt c.*240 . . . . . . g.68971 ggaggaaagtgcctgcctctggtccgagccgcctcggttctgaagcgagtgctcctgctt c.*300 . . . . . . g.69031 accttgctctaggctgtctgcagaagcacctgccggtggcactcagcacctccttgtgct c.*360 . . . . . . g.69091 agagccctccatcaccttcacgctgtcccaccatgggccaggaaccaaaccagcactggg c.*420 . . . . . . g.69151 ttctactgctgtggggtaaactaactcagtggaatagggctggttactttgggctgtcca c.*480 . . . . . . g.69211 actcataagtttggctgcattttgaaaaaagctgatctaaataaaggcatgtgtatggct c.*540 g.69215 ggtc c.*544 (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 Calpain 3, (p94) 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 variants, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.

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