tropomyosin 1 (alpha) (TPM1) - coding DNA reference sequence

(used for mutation description)

(last modified July 23, 2010)

This file was created to facilitate the description of sequence variants in the TPM1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_007557.1, covering TPM1 transcript variant-1 (NM_001018005.1). Alternatively spliced exons 2a (derived from intron 1) and 6a (derived from intron 5) are present in a major fraction of transcripts; variant-2 (NM_001018007.1), -3 (NM_001018004.1), -4 (NM_001018006.1), -5 (NM_000366.5), -7 (NM_001018020.1). Exon 9 has an alternative splice donor site in intron 09. Transcript variant-6 (NM_001018008.1) uses an alternative promoter/exon1b and alternative 3'-terminal exon 10b, downstream. Transcript variants variant-2, -3, -4 and -7 use an even further downstream alternative 3'-terminal exon 10c.

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

 (upstream sequence)
                                                   .                g.5011
                                                  ggaaggggggc       c.-181

 .         .         .         .         .         .                g.5071
 aggagaaaaaagcttttccaaaaaagtattggctgtcttgaggaatgcggtcgccccctt       c.-121

 .         .         .         .         .         .                g.5131
 gggaaagtacatatctgggagaagcaggcggctccgcgctcgcactcccgctcctccgcc       c.-61

 .         .         .         .         .         .                g.5191
 cgaccgcgcgctcgccccgccgctcctgctgcagccccagggcccctcgccgccgccacc       c.-1

          .         .         .         .         .         .       g.5251
 ATGGACGCCATCAAGAAGAAGATGCAGATGCTGAAGCTCGACAAGGAGAACGCCTTGGAT       c.60
 M  D  A  I  K  K  K  M  Q  M  L  K  L  D  K  E  N  A  L  D         p.20

          .         .         .         .         .     | 02   .    g.6394
 CGAGCTGAGCAGGCGGAGGCCGACAAGAAGGCGGCGGAAGACAGGAGCAAGCAG | CTGGAA    c.120
 R  A  E  Q  A  E  A  D  K  K  A  A  E  D  R  S  K  Q   | L  E      p.40
                         alternatively spliced exon 2a  ^

          .         .         .         .         .         .       g.6454
 GATGAGCTGGTGTCACTGCAAAAGAAACTCAAGGGCACCGAAGATGAACTGGACAAATAC       c.180
 D  E  L  V  S  L  Q  K  K  L  K  G  T  E  D  E  L  D  K  Y         p.60

          .         .         .         .         .         .       g.6514
 TCTGAGGCTCTCAAAGATGCCCAGGAGAAGCTGGAGCTGGCAGAGAAAAAGGCCACCGAT       c.240
 S  E  A  L  K  D  A  Q  E  K  L  E  L  A  E  K  K  A  T  D         p.80

  | 03       .         .         .         .         .         .    g.19406
  | GCTGAAGCCGACGTAGCTTCTCTGAACAGACGCATCCAGCTGGTTGAGGAAGAGTTGGAT    c.300
  | A  E  A  D  V  A  S  L  N  R  R  I  Q  L  V  E  E  E  L  D      p.100
  ^  alternative promoter/exon 1b

          .         .         .         .         .         .       g.19466
 CGTGCCCAGGAGCGTCTGGCAACAGCTTTGCAGAAGCTGGAGGAAGCTGAGAAGGCAGCA       c.360
 R  A  Q  E  R  L  A  T  A  L  Q  K  L  E  E  A  E  K  A  A         p.120

          .     | 04   .         .         .         .         .    g.21970
 GATGAGAGTGAGAG | AGGCATGAAAGTCATTGAGAGTCGAGCCCAAAAAGATGAAGAAAAA    c.420
 D  E  S  E  R  |  G  M  K  V  I  E  S  R  A  Q  K  D  E  E  K      p.140

          .         .         .         .         .         .       g.22030
 ATGGAAATTCAGGAGATCCAACTGAAAGAGGCCAAGCACATTGCTGAAGATGCCGACCGC       c.480
 M  E  I  Q  E  I  Q  L  K  E  A  K  H  I  A  E  D  A  D  R         p.160

          .   | 05     .         .         .         .         .    g.23278
 AAATATGAAGAG | GTGGCCCGTAAGCTGGTCATCATTGAGAGCGACCTGGAACGTGCAGAG    c.540
 K  Y  E  E   | V  A  R  K  L  V  I  I  E  S  D  L  E  R  A  E      p.180

          .         .    | 06    .         .         .         .    g.24111
 GAGCGGGCTGAGCTCTCAGAAGG | CAAATGTGCCGAGCTTGAAGAAGAATTGAAAACTGTG    c.600
 E  R  A  E  L  S  E  G  |  K  C  A  E  L  E  E  E  L  K  T  V      p.200
                         ^  alternatively spliced exon 06a

          .         .         .          | 07        .         .    g.24597
 ACGAACAACTTGAAGTCACTGGAGGCTCAGGCTGAGAAG | TACTCGCAGAAGGAAGACAGA    c.660
 T  N  N  L  K  S  L  E  A  Q  A  E  K   | Y  S  Q  K  E  D  R      p.220

          .         .         .         .   | 08     .         .    g.24955
 TATGAGGAAGAGATCAAGGTCCTTTCCGACAAGCTGAAGGAG | GCTGAGACTCGGGCTGAG    c.720
 Y  E  E  E  I  K  V  L  S  D  K  L  K  E   | A  E  T  R  A  E      p.240

          .         .         .         .         .   | 09     .    g.26433
 TTTGCGGAGAGGTCAGTAACTAAATTGGAGAAAAGCATTGATGACTTAGAAG | ACGAGCTG    c.780
 F  A  E  R  S  V  T  K  L  E  K  S  I  D  D  L  E  D |   E  L      p.260

          .         .         .         .         .         .       g.26493
 TACGCTCAGAAACTGAAGTACAAAGCCATCAGCGAGGAGCTGGACCACGCTCTCAACGAT       c.840
 Y  A  Q  K  L  K  Y  K  A  I  S  E  E  L  D  H  A  L  N  D         p.280

          .  | 10                                                   g.28306
 ATGACTTCCAT | ATAA                                                 c.855
 M  T  S  I  |  X                                                   p.284
             ^  2 alternative 3'-terminal exons 10b and 10c and alternative exon 9 splice site

          .         .         .         .         .         .       g.28366
 gtttctttgcttcacttctcccaagactccctcgtcgagctggatgtcccacctctctga       c.*60

          .         .         .         .         .         .       g.28426
 gctctgcatttgtctattctccagctgaccctggttctctctcttagcatcctgccttag       c.*120

          .         .         .         .         .         .       g.28486
 agccaggcacacactgtgctttctattgtacagaagctcttcgtttcagtgtcaaataaa       c.*180

          .                                                         g.28500
 cactgtgtaagcta                                                     c.*194

 (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 Tropomyosin 1 (alpha) 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.