homeobox D9 (HOXD9) - coding DNA reference sequence

(used for variant description)

(last modified August 22, 2016)

This file was created to facilitate the description of sequence variants on transcript NM_014213.3 in the HOXD9 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_009225.1, covering HOXD9 transcript NM_014213.3.

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

 (upstream sequence)
                                         .         .                g.5024
                                     cgcgaccaatggtggaggctgcag       c.-61

 .         .         .         .         .         .                g.5084
 cctgcgaactagtcggtggctcgggcgccggcggggagctgctcggcggcggacagtgta       c.-1

          .         .         .         .         .         .       g.5144
 ATGTTGGGTGGGAGTGCGGGACGCCTCAAAATGTCTTCCAGTGGCACCCTCAGCAACTAC       c.60
 M  L  G  G  S  A  G  R  L  K  M  S  S  S  G  T  L  S  N  Y         p.20

          .         .         .         .         .         .       g.5204
 TACGTGGACTCGCTTATAGGCCATGAGGGCGACGAGGTGTTCGCGGCGCGCTTCGGGCCG       c.120
 Y  V  D  S  L  I  G  H  E  G  D  E  V  F  A  A  R  F  G  P         p.40

          .         .         .         .         .         .       g.5264
 CCGGGGCCAGGCGCGCAGGGCCGGCCTGCAGGTGTGGCTGATGGCCCGGCCGCCACCGCC       c.180
 P  G  P  G  A  Q  G  R  P  A  G  V  A  D  G  P  A  A  T  A         p.60

          .         .         .         .         .         .       g.5324
 GCCGAGTTCGCCTCGTGTAGTTTTGCCCCCAGATCGGCCGTGTTCTCTGCCTCGTGGTCC       c.240
 A  E  F  A  S  C  S  F  A  P  R  S  A  V  F  S  A  S  W  S         p.80

          .         .         .         .         .         .       g.5384
 GCGGTGCCCTCCCAGCCCCCGGCAGCGGCGGCGATGAGCGGCCTCTACCACCCGTACGTT       c.300
 A  V  P  S  Q  P  P  A  A  A  A  M  S  G  L  Y  H  P  Y  V         p.100

          .         .         .         .         .         .       g.5444
 CCCCCGCCGCCCCTGGCCGCCTCTGCCTCCGAGCCCGGCCGCTACGTGCGCTCCTGGATG       c.360
 P  P  P  P  L  A  A  S  A  S  E  P  G  R  Y  V  R  S  W  M         p.120

          .         .         .         .         .         .       g.5504
 GAGCCGCTGCCCGGCTTCCCGGGCGGTGCGGGCGGTGGCGGTGGTGGTGGAGGCGGCGGT       c.420
 E  P  L  P  G  F  P  G  G  A  G  G  G  G  G  G  G  G  G  G         p.140

          .         .         .         .         .         .       g.5564
 CCGGGCCGCGGTCCCAGCCCTGGCCCCAGCGGCCCAGCCAACGGGCGCCACTACGGGATT       c.480
 P  G  R  G  P  S  P  G  P  S  G  P  A  N  G  R  H  Y  G  I         p.160

          .         .         .         .         .         .       g.5624
 AAGCCTGAAACCCGAGCGGCCCCGGCCCCCGCCACGGCCGCCTCCACCACCTCCTCCTCC       c.540
 K  P  E  T  R  A  A  P  A  P  A  T  A  A  S  T  T  S  S  S         p.180

          .         .         .         .         .         .       g.5684
 TCCACTTCCTTATCCTCCTCCTCCAAACGGACTGAGTGCTCCGTGGCCCGGGAGTCCCAG       c.600
 S  T  S  L  S  S  S  S  K  R  T  E  C  S  V  A  R  E  S  Q         p.200

          .         .         .         .         .         .       g.5744
 GGGAGCAGCGGCCCCGAGTTCTCGTGCAACTCGTTCCTGCAGGAGAAGGCGGCAGCGGCG       c.660
 G  S  S  G  P  E  F  S  C  N  S  F  L  Q  E  K  A  A  A  A         p.220

          .         .         .         .         .         .       g.5804
 ACGGGGGGAACCGGGCCTGGGGCAGGGATCGGGGCCGCGACTGGGACGGGCGGCTCGTCG       c.720
 T  G  G  T  G  P  G  A  G  I  G  A  A  T  G  T  G  G  S  S         p.240

          .         .         .         .         .         .       g.5864
 GAGCCCTCAGCTTGCAGCGACCACCCGATCCCAGGCTGTTCGCTGAAGGAGGAGGAGAAG       c.780
 E  P  S  A  C  S  D  H  P  I  P  G  C  S  L  K  E  E  E  K         p.260

          .         .         .        | 02.         .         .    g.6272
 CAGCATTCGCAGCCGCAGCAGCAGCAACTTGACCCAA | ACAACCCCGCCGCGAACTGGATC    c.840
 Q  H  S  Q  P  Q  Q  Q  Q  L  D  P  N |   N  P  A  A  N  W  I      p.280

          .         .         .         .         .         .       g.6332
 CACGCTCGCTCCACCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTTGAGCTG       c.900
 H  A  R  S  T  R  K  K  R  C  P  Y  T  K  Y  Q  T  L  E  L         p.300

          .         .         .         .         .         .       g.6392
 GAGAAAGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGGCCAGG       c.960
 E  K  E  F  L  F  N  M  Y  L  T  R  D  R  R  Y  E  V  A  R         p.320

          .         .         .         .         .         .       g.6452
 ATTCTCAACCTAACAGAGAGACAGGTCAAAATCTGGTTTCAGAACCGTAGGATGAAAATG       c.1020
 I  L  N  L  T  E  R  Q  V  K  I  W  F  Q  N  R  R  M  K  M         p.340

          .         .         .                                     g.6491
 AAAAAGATGAGCAAGGAGAAATGCCCCAAAGGAGACTGA                            c.1059
 K  K  M  S  K  E  K  C  P  K  G  D  X                              p.352

          .         .         .         .         .         .       g.6551
 cccggcgcggtgctggcgggagcgctcaagggcagcggatttgttgttgttgctgttttc       c.*60

          .         .         .         .         .         .       g.6611
 ctttgtgggtgtttggtgcttgatttccagaaactctccagcgacttggacttcttcttc       c.*120

          .         .         .         .         .         .       g.6671
 tttttttttttctttttagatagaagtgactgtgtggttggtctctgaggtatttggggg       c.*180

          .         .         .         .         .         .       g.6731
 actctgtatttgctcgtttacgtgttggaaaaaccaagtggctttggggtttcgccctat       c.*240

          .         .         .         .         .         .       g.6791
 cccactccctctctttcctgctccattggttccttaagaaatgctatattttgtgagtgc       c.*300

          .         .         .         .         .         .       g.6851
 aagctggcttggggagccctctcttgtgtaaatgtcccccatgtttctgaaaagtgctgt       c.*360

          .         .         .         .         .         .       g.6911
 agtttagtcccctcacccccagcactgcccaaacaggggccaagtgcgccccaattccaa       c.*420

          .         .         .         .         .         .       g.6971
 gaatgaaggcagagcgacaacagtgcggacaccccggctgctagcccacggtgaagcccg       c.*480

          .         .         .         .         .         .       g.7031
 gcggggttgcccaccagttgcgaaagccccctttcctcagggagcacgcgggacctcggt       c.*540

          .         .         .         .         .         .       g.7091
 ggagatctccagtgaggcttagaggagcccagggcctcgggcgggttggggtttgtcctc       c.*600

          .         .         .         .         .         .       g.7151
 agtgcattggacgcgctgctctctcccctgaaggctgggctcgcgtgggcggccgcgggt       c.*660

          .         .         .         .         .         .       g.7211
 ggtggccctcccggttcctgcccgaggaccagttgtaaatgttactgcttcctactaata       c.*720

          .         .                                               g.7233
 aatgctgacctgatcaaatgga                                             c.*742

 (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 Homeobox D9 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.