paired-like homeodomain 2 (PITX2) - coding DNA reference sequence

(used for variant description)

(last modified August 10, 2020)


This file was created to facilitate the description of sequence variants on transcript NM_000325.5 in the PITX2 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_007120.1, covering PITX2 transcript NM_000325.5.


Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                               .         .         .                g.24063
                       gttaggccaacagggaagcgcggagccgcagatctggt       c.-601

 .         .         .         .         .         .                g.24123
 ccgtcgctcgcctgggtgcctggagctgagctgcggcaaggcccggctcctgttcgaccg       c.-541

 .         .         .         .         .         .                g.24183
 cccgaggggtgtgcgtgtgcgcgttgcggagggtgcgctcagagggccgcgtcgtggctg       c.-481

 .         .         .         .         .         .                g.24243
 cagcggctgctgccgccgcaggggatctaatatcacctacctgtccctgtcactcttgac       c.-421

 .         .         .         .         .         .                g.24303
 acttctctgtcagggctgccgcgtggggggggggcgggcagagcgcggtcggcgttagct       c.-361

 .         .         .         .         .         .                g.24363
 ttccttattggaggggttcttgggggagggagggagagaagaagggggtctttgcccact       c.-301

 .         .         .         .         .         .                g.24423
 cttgtttcgctttggagcttggaagcctgctccctaaagacgctctgagtggtgcccttc       c.-241

 .         .         .         .         .         .                g.24483
 tgcccacatcccatgtcttcgtttgcccgctgactttccgtctccggactttttcgcttg       c.-181

 .         .         .         .         .         .                g.24543
 agccttccggaggagacgggggcagcttggcttgagaactcggcgggggttgcgtcccct       c.-121

 .         .         .         .         .         .                g.24603
 ggctctccccgcagcggggaaactccgcgcctagagcgcgacccggagcgggcagcggcg       c.-61

 .         .         .         .         .         .                g.24663
 gctacgggggctcggcggggcagtagccaaggactagtagagcgtcgcgctccctcgtcc       c.-1

          .         .         .         .         .         .       g.24723
 ATGAACTGCATGAAAGGCCCGCTTCACTTGGAGCACCGAGCAGCGGGGACCAAGCTGTCG       c.60
 M  N  C  M  K  G  P  L  H  L  E  H  R  A  A  G  T  K  L  S         p.20

          .         .         .         .         .         .       g.24783
 GCCGTCTCCTCATCTTCCTGTCACCATCCCCAGCCGTTAGCCATGGCTTCGGTTCTGGCT       c.120
 A  V  S  S  S  S  C  H  H  P  Q  P  L  A  M  A  S  V  L  A         p.40

          .         .         .         .         .         .       g.24843
 CCCGGTCAGCCCCGGTCGCTGGACTCCTCCAAGCACAGGCTGGAGGTGCACACCATCTCC       c.180
 P  G  Q  P  R  S  L  D  S  S  K  H  R  L  E  V  H  T  I  S         p.60

          .         .      | 02  .         .         .         .    g.25789
 GACACCTCCAGCCCGGAGGCCGCAG | AGAAAGATAAAAGCCAGCAGGGGAAGAATGAGGAC    c.240
 D  T  S  S  P  E  A  A  E |   K  D  K  S  Q  Q  G  K  N  E  D      p.80

          .         .         .         .         .         .       g.25849
 GTGGGCGCCGAGGACCCGTCTAAGAAGAAGCGGCAAAGGCGGCAGCGGACTCACTTTACC       c.300
 V  G  A  E  D  P  S  K  K  K  R  Q  R  R  Q  R  T  H  F  T         p.100

          .         .         .         .         .         .       g.25909
 AGCCAGCAGCTCCAGGAGCTGGAGGCCACTTTCCAGAGGAACCGCTACCCGGACATGTCC       c.360
 S  Q  Q  L  Q  E  L  E  A  T  F  Q  R  N  R  Y  P  D  M  S         p.120

          .         .         .         .         .  | 03      .    g.28444
 ACACGCGAAGAAATCGCTGTGTGGACCAACCTTACGGAAGCCCGAGTCCGG | GTTTGGTTC    c.420
 T  R  E  E  I  A  V  W  T  N  L  T  E  A  R  V  R   | V  W  F      p.140

          .         .         .         .         .         .       g.28504
 AAGAATCGTCGGGCCAAATGGAGAAAGAGGGAGCGCAACCAGCAGGCCGAGCTATGCAAG       c.480
 K  N  R  R  A  K  W  R  K  R  E  R  N  Q  Q  A  E  L  C  K         p.160

          .         .         .         .         .         .       g.28564
 AATGGCTTCGGGCCGCAGTTCAATGGGCTCATGCAGCCCTACGACGACATGTACCCAGGC       c.540
 N  G  F  G  P  Q  F  N  G  L  M  Q  P  Y  D  D  M  Y  P  G         p.180

          .         .         .         .         .         .       g.28624
 TATTCCTACAACAACTGGGCCGCCAAGGGCCTTACATCCGCCTCCCTATCCACCAAGAGC       c.600
 Y  S  Y  N  N  W  A  A  K  G  L  T  S  A  S  L  S  T  K  S         p.200

          .         .         .         .         .         .       g.28684
 TTCCCCTTCTTCAACTCTATGAACGTCAACCCCCTGTCATCACAGAGCATGTTTTCCCCA       c.660
 F  P  F  F  N  S  M  N  V  N  P  L  S  S  Q  S  M  F  S  P         p.220

          .         .         .         .         .         .       g.28744
 CCCAACTCTATCTCGTCCATGAGCATGTCGTCCAGCATGGTGCCCTCAGCAGTGACAGGC       c.720
 P  N  S  I  S  S  M  S  M  S  S  S  M  V  P  S  A  V  T  G         p.240

          .         .         .         .         .         .       g.28804
 GTCCCGGGCTCCAGTCTCAACAGCCTGAATAACTTGAACAACCTGAGTAGCCCGTCGCTG       c.780
 V  P  G  S  S  L  N  S  L  N  N  L  N  N  L  S  S  P  S  L         p.260

          .         .         .         .         .         .       g.28864
 AATTCCGCGGTGCCGACGCCTGCCTGTCCTTACGCGCCGCCGACTCCTCCGTATGTTTAT       c.840
 N  S  A  V  P  T  P  A  C  P  Y  A  P  P  T  P  P  Y  V  Y         p.280

          .         .         .         .         .         .       g.28924
 AGGGACACGTGTAACTCGAGCCTGGCCAGCCTGAGACTGAAAGCAAAGCAGCACTCCAGC       c.900
 R  D  T  C  N  S  S  L  A  S  L  R  L  K  A  K  Q  H  S  S         p.300

          .         .         .         .         .         .       g.28984
 TTCGGCTACGCCAGCGTGCAGAACCCGGCCTCCAACCTGAGTGCTTGCCAGTATGCAGTG       c.960
 F  G  Y  A  S  V  Q  N  P  A  S  N  L  S  A  C  Q  Y  A  V         p.320

          .                                                         g.28999
 GACCGGCCCGTGTGA                                                    c.975
 D  R  P  V  X                                                      p.324

          .         .         .         .         .         .       g.29059
 gccgcacccacagcgccgggatcctaggaccttgccggatggggcaactccgcccttgaa       c.*60

          .         .         .         .         .         .       g.29119
 agactgggaattatgctagaaggtcgtgggcactaaagaaagggagagaaagagaagcta       c.*120

          .         .         .         .         .         .       g.29179
 tatagagaaaaggaaaccactgaatcaaagagagagctcctttgatttcaaagggatgtc       c.*180

          .         .         .         .         .         .       g.29239
 ctcagtgtctgacatctttcactacaagtatttctaacagttgcaaggacacatacacaa       c.*240

          .         .         .         .         .         .       g.29299
 acaaatgtttgactggatatgacattttaacattactataagcttgttattttttaagtt       c.*300

          .         .         .         .         .         .       g.29359
 tagcattgttaacatttaaatgactgaaaggatgtatatatatcgaaatgtcaaattaat       c.*360

          .         .         .         .         .         .       g.29419
 tttataaaagcagttgttagtaatatcacaacagtgtttttaaaggttaggctttaaaat       c.*420

          .         .         .         .         .         .       g.29479
 aaagcatgttatacagaagcgattaggatttttcgcttgcgagcaagggagtgtatatac       c.*480

          .         .         .         .         .         .       g.29539
 taaatgccacactgtatgtttctaacatattattattattataaaaaatgtgtgaatatc       c.*540

          .         .         .         .         .         .       g.29599
 agttttagaatagtttctctggtggatgcaatgatgtttctgaaactgctatgtacaacc       c.*600

          .         .         .         .         .         .       g.29659
 taccctgtgtataacatttcgtacaatattattgttttacttttcagcaaatatgaaaca       c.*660

          .         .         .         .                           g.29701
 aatgtgttttatttcatgggagtaaaatatactgcatacaaa                         c.*702

 (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 Paired-like homeodomain 2 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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