NK2 homeobox 5 (NKX2-5) - coding DNA reference sequence

(used for variant description)

(last modified January 23, 2015)

This file was created to facilitate the description of sequence variants on transcript NM_004387.3 in the NKX2-5 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_013340.1, covering NKX2-5 transcript NM_004387.3.

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

 (upstream sequence)
                     .         .         .         .                g.5049
            gctcctgtcatcgaggcccctggcccaatggcaggctgagtccccctcc       c.-181

 .         .         .         .         .         .                g.5109
 tctggcctggtcccgcctctcctgccccttgtgctcagcgctacctgctgcccggacaca       c.-121

 .         .         .         .         .         .                g.5169
 tccagagctggccgacgggtgcgcgggcgggcggcggcaccatgcagggaagctgccagg       c.-61

 .         .         .         .         .         .                g.5229
 ggccgtgggcagcgccgctttctgccgcccacctggcgctgtgagactggcgctgccacc       c.-1

          .         .         .         .         .         .       g.5289
 ATGTTCCCCAGCCCTGCTCTCACGCCCACGCCCTTCTCAGTCAAAGACATCCTAAACCTG       c.60
 M  F  P  S  P  A  L  T  P  T  P  F  S  V  K  D  I  L  N  L         p.20

          .         .         .         .         .         .       g.5349
 GAACAGCAGCAGCGCAGCCTGGCTGCCGCCGGAGAGCTCTCTGCCCGCCTGGAGGCGACC       c.120
 E  Q  Q  Q  R  S  L  A  A  A  G  E  L  S  A  R  L  E  A  T         p.40

          .         .         .         .         .         .       g.5409
 CTGGCGCCCTCCTCCTGCATGCTGGCCGCCTTCAAGCCAGAGGCCTACGCTGGGCCCGAG       c.180
 L  A  P  S  S  C  M  L  A  A  F  K  P  E  A  Y  A  G  P  E         p.60

          .         .         .         .         .         .       g.5469
 GCGGCTGCGCCGGGCCTCCCAGAGCTGCGCGCAGAGCTGGGCCGCGCGCCTTCACCGGCC       c.240
 A  A  A  P  G  L  P  E  L  R  A  E  L  G  R  A  P  S  P  A         p.80

          .         .         .         .         .         .       g.5529
 AAGTGTGCGTCTGCCTTTCCCGCCGCCCCCGCCTTCTATCCACGTGCCTACAGCGACCCC       c.300
 K  C  A  S  A  F  P  A  A  P  A  F  Y  P  R  A  Y  S  D  P         p.100

          .         .         .     | 02   .         .         .    g.7129
 GACCCAGCCAAGGACCCTAGAGCCGAAAAGAAAG | AGCTGTGCGCGCTGCAGAAGGCGGTG    c.360
 D  P  A  K  D  P  R  A  E  K  K  E |   L  C  A  L  Q  K  A  V      p.120

          .         .         .         .         .         .       g.7189
 GAGCTGGAGAAGACAGAGGCGGACAACGCGGAGCGGCCCCGGGCGCGACGGCGGAGGAAG       c.420
 E  L  E  K  T  E  A  D  N  A  E  R  P  R  A  R  R  R  R  K         p.140

          .         .         .         .         .         .       g.7249
 CCGCGCGTGCTCTTCTCGCAGGCGCAGGTCTATGAGCTGGAGCGGCGCTTCAAGCAGCAG       c.480
 P  R  V  L  F  S  Q  A  Q  V  Y  E  L  E  R  R  F  K  Q  Q         p.160

          .         .         .         .         .         .       g.7309
 CGGTACCTGTCGGCCCCCGAACGCGACCAGCTGGCCAGCGTGCTGAAACTCACGTCCACG       c.540
 R  Y  L  S  A  P  E  R  D  Q  L  A  S  V  L  K  L  T  S  T         p.180

          .         .         .         .         .         .       g.7369
 CAGGTCAAGATCTGGTTCCAGAACCGGCGCTACAAGTGCAAGCGGCAGCGGCAGGACCAG       c.600
 Q  V  K  I  W  F  Q  N  R  R  Y  K  C  K  R  Q  R  Q  D  Q         p.200

          .         .         .         .         .         .       g.7429
 ACTCTGGAGCTGGTGGGGCTGCCCCCGCCGCCGCCGCCGCCTGCCCGCAGGATCGCGGTG       c.660
 T  L  E  L  V  G  L  P  P  P  P  P  P  P  A  R  R  I  A  V         p.220

          .         .         .         .         .         .       g.7489
 CCAGTGCTGGTGCGCGATGGCAAGCCATGCCTAGGGGACTCGGCGCCCTACGCGCCTGCC       c.720
 P  V  L  V  R  D  G  K  P  C  L  G  D  S  A  P  Y  A  P  A         p.240

          .         .         .         .         .         .       g.7549
 TACGGCGTGGGCCTCAATCCCTACGGTTATAACGCCTACCCCGCCTATCCGGGTTACGGC       c.780
 Y  G  V  G  L  N  P  Y  G  Y  N  A  Y  P  A  Y  P  G  Y  G         p.260

          .         .         .         .         .         .       g.7609
 GGCGCGGCCTGCAGCCCTGGCTACAGCTGCACTGCCGCTTACCCCGCCGGGCCTTCCCCA       c.840
 G  A  A  C  S  P  G  Y  S  C  T  A  A  Y  P  A  G  P  S  P         p.280

          .         .         .         .         .         .       g.7669
 GCGCAGCCGGCCACTGCCGCCGCCAACAACAACTTCGTGAACTTCGGCGTCGGGGACTTG       c.900
 A  Q  P  A  T  A  A  A  N  N  N  F  V  N  F  G  V  G  D  L         p.300

          .         .         .         .         .         .       g.7729
 AATGCGGTTCAGAGCCCCGGGATTCCGCAGAGCAACTCGGGAGTGTCCACGCTGCATGGT       c.960
 N  A  V  Q  S  P  G  I  P  Q  S  N  S  G  V  S  T  L  H  G         p.320

          .                                                         g.7744
 ATCCGAGCCTGGTAG                                                    c.975
 I  R  A  W  X                                                      p.324

          .         .         .         .         .         .       g.7804
 ggaagggacccgcgtggcgcgaccctgaccgatcccacctcaacagctccctgactctcg       c.*60

          .         .         .         .         .         .       g.7864
 gggggagaaggggctcccaacatgaccctgagtcccctggattttgcattcactcctgcg       c.*120

          .         .         .         .         .         .       g.7924
 gagacctaggaactttttctgtcccacgcgcgtttgttcttgcgcacgggagagtttgtg       c.*180

          .         .         .         .         .         .       g.7984
 gcggcgattatgcagcgtgcaatgagtgatcctgcagcctggtgtcttagctgtcccccc       c.*240

          .         .         .         .         .         .       g.8044
 aggagtgccctccgagagtccatgggcacccccggttggaactgggactgagctcgggca       c.*300

          .         .         .         .         .         .       g.8104
 cgcagggcctgagatctggccgcccattccgcgagccagggccgggcgcccgggcctttg       c.*360

          .         .         .         .         .         .       g.8164
 ctatctcgccgtcgcccgcccacgcacccacccgtatttatgtttttacctattgctgta       c.*420

          .         .         .         .                           g.8209
 agaaatgacgatccccttcccattaaagagagtgcgttgaccccg                      c.*465

 (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 NK2 homeobox 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 variants, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.