forkhead box C1 (FOXC1) - coding DNA reference sequence

(used for variant description)

(last modified March 18, 2016)

This file was created to facilitate the description of sequence variants on transcript NM_001453.2 in the FOXC1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_009368.1, covering FOXC1 transcript NM_001453.2.

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

 (upstream sequence)
          .         .         .         .         .         .       g.60
 ATGCAGGCGCGCTACTCCGTGTCCAGCCCCAACTCCCTGGGAGTGGTGCCCTACCTCGGC       c.60
 M  Q  A  R  Y  S  V  S  S  P  N  S  L  G  V  V  P  Y  L  G         p.20

          .         .         .         .         .         .       g.120
 GGCGAGCAGAGCTACTACCGCGCGGCGGCCGCGGCGGCCGGGGGCGGCTACACCGCCATG       c.120
 G  E  Q  S  Y  Y  R  A  A  A  A  A  A  G  G  G  Y  T  A  M         p.40

          .         .         .         .         .         .       g.180
 CCGGCCCCCATGAGCGTGTACTCGCACCCTGCGCACGCCGAGCAGTACCCGGGCGGCATG       c.180
 P  A  P  M  S  V  Y  S  H  P  A  H  A  E  Q  Y  P  G  G  M         p.60

          .         .         .         .         .         .       g.240
 GCCCGCGCCTACGGGCCCTACACGCCGCAGCCGCAGCCCAAGGACATGGTGAAGCCGCCC       c.240
 A  R  A  Y  G  P  Y  T  P  Q  P  Q  P  K  D  M  V  K  P  P         p.80

          .         .         .         .         .         .       g.300
 TATAGCTACATCGCGCTCATCACCATGGCCATCCAGAACGCCCCGGACAAGAAGATCACC       c.300
 Y  S  Y  I  A  L  I  T  M  A  I  Q  N  A  P  D  K  K  I  T         p.100

          .         .         .         .         .         .       g.360
 CTGAACGGCATCTACCAGTTCATCATGGACCGCTTCCCCTTCTACCGGGACAACAAGCAG       c.360
 L  N  G  I  Y  Q  F  I  M  D  R  F  P  F  Y  R  D  N  K  Q         p.120

          .         .         .         .         .         .       g.420
 GGCTGGCAGAACAGCATCCGCCACAACCTCTCGCTCAACGAGTGCTTCGTCAAGGTGCCG       c.420
 G  W  Q  N  S  I  R  H  N  L  S  L  N  E  C  F  V  K  V  P         p.140

          .         .         .         .         .         .       g.480
 CGCGACGACAAGAAGCCGGGCAAGGGCAGCTACTGGACGCTGGACCCGGACTCCTACAAC       c.480
 R  D  D  K  K  P  G  K  G  S  Y  W  T  L  D  P  D  S  Y  N         p.160

          .         .         .         .         .         .       g.540
 ATGTTCGAGAACGGCAGCTTCCTGCGGCGGCGGCGGCGCTTCAAGAAGAAGGACGCGGTG       c.540
 M  F  E  N  G  S  F  L  R  R  R  R  R  F  K  K  K  D  A  V         p.180

          .         .         .         .         .         .       g.600
 AAGGACAAGGAGGAGAAGGACAGGCTGCACCTCAAGGAGCCGCCCCCGCCCGGCCGCCAG       c.600
 K  D  K  E  E  K  D  R  L  H  L  K  E  P  P  P  P  G  R  Q         p.200

          .         .         .         .         .         .       g.660
 CCCCCGCCCGCGCCGCCGGAGCAGGCCGACGGCAACGCGCCCGGTCCGCAGCCGCCGCCC       c.660
 P  P  P  A  P  P  E  Q  A  D  G  N  A  P  G  P  Q  P  P  P         p.220

          .         .         .         .         .         .       g.720
 GTGCGCATCCAGGACATCAAGACCGAGAACGGTACGTGCCCCTCGCCGCCCCAGCCCCTG       c.720
 V  R  I  Q  D  I  K  T  E  N  G  T  C  P  S  P  P  Q  P  L         p.240

          .         .         .         .         .         .       g.780
 TCCCCGGCCGCCGCCCTGGGCAGCGGCAGCGCCGCCGCGGTGCCCAAGATCGAGAGCCCC       c.780
 S  P  A  A  A  L  G  S  G  S  A  A  A  V  P  K  I  E  S  P         p.260

          .         .         .         .         .         .       g.840
 GACAGCAGCAGCAGCAGCCTGTCCAGCGGGAGCAGCCCCCCGGGCAGCCTGCCGTCGGCG       c.840
 D  S  S  S  S  S  L  S  S  G  S  S  P  P  G  S  L  P  S  A         p.280

          .         .         .         .         .         .       g.900
 CGGCCGCTCAGCCTGGACGGTGCGGATTCCGCGCCGCCGCCGCCCGCGCCCTCCGCCCCG       c.900
 R  P  L  S  L  D  G  A  D  S  A  P  P  P  P  A  P  S  A  P         p.300

          .         .         .         .         .         .       g.960
 CCGCCGCACCATAGCCAGGGCTTCAGCGTGGACAACATCATGACGTCGCTGCGGGGGTCG       c.960
 P  P  H  H  S  Q  G  F  S  V  D  N  I  M  T  S  L  R  G  S         p.320

          .         .         .         .         .         .       g.1020
 CCGCAGAGCGCGGCCGCGGAGCTCAGCTCCGGCCTTCTGGCCTCGGCGGCCGCGTCCTCG       c.1020
 P  Q  S  A  A  A  E  L  S  S  G  L  L  A  S  A  A  A  S  S         p.340

          .         .         .         .         .         .       g.1080
 CGCGCGGGGATCGCACCCCCGCTGGCGCTCGGCGCCTACTCGCCCGGCCAGAGCTCCCTC       c.1080
 R  A  G  I  A  P  P  L  A  L  G  A  Y  S  P  G  Q  S  S  L         p.360

          .         .         .         .         .         .       g.1140
 TACAGCTCCCCCTGCAGCCAGACCTCCAGCGCGGGCAGCTCGGGCGGCGGCGGCGGCGGC       c.1140
 Y  S  S  P  C  S  Q  T  S  S  A  G  S  S  G  G  G  G  G  G         p.380

          .         .         .         .         .         .       g.1200
 GCGGGGGCCGCGGGGGGCGCGGGCGGCGCCGGGACCTACCACTGCAACCTGCAAGCCATG       c.1200
 A  G  A  A  G  G  A  G  G  A  G  T  Y  H  C  N  L  Q  A  M         p.400

          .         .         .         .         .         .       g.1260
 AGCCTGTACGCGGCCGGCGAGCGCGGGGGCCACTTGCAGGGCGCGCCCGGGGGCGCGGGC       c.1260
 S  L  Y  A  A  G  E  R  G  G  H  L  Q  G  A  P  G  G  A  G         p.420

          .         .         .         .         .         .       g.1320
 GGCTCGGCCGTGGACGACCCCCTGCCCGACTACTCTCTGCCTCCGGTCACCAGCAGCAGC       c.1320
 G  S  A  V  D  D  P  L  P  D  Y  S  L  P  P  V  T  S  S  S         p.440

          .         .         .         .         .         .       g.1380
 TCGTCGTCCCTGAGTCACGGCGGCGGCGGCGGCGGCGGCGGGGGAGGCCAGGAGGCCGGC       c.1380
 S  S  S  L  S  H  G  G  G  G  G  G  G  G  G  G  Q  E  A  G         p.460

          .         .         .         .         .         .       g.1440
 CACCACCCTGCGGCCCACCAAGGCCGCCTCACCTCGTGGTACCTGAACCAGGCGGGCGGA       c.1440
 H  H  P  A  A  H  Q  G  R  L  T  S  W  Y  L  N  Q  A  G  G         p.480

          .         .         .         .         .         .       g.1500
 GACCTGGGCCACTTGGCGAGCGCGGCGGCGGCGGCGGCGGCCGCAGGCTACCCGGGCCAG       c.1500
 D  L  G  H  L  A  S  A  A  A  A  A  A  A  A  G  Y  P  G  Q         p.500

          .         .         .         .         .         .       g.1560
 CAGCAGAACTTCCACTCGGTGCGGGAGATGTTCGAGTCACAGAGGATCGGCTTGAACAAC       c.1560
 Q  Q  N  F  H  S  V  R  E  M  F  E  S  Q  R  I  G  L  N  N         p.520

          .         .         .         .         .         .       g.1620
 TCTCCAGTGAACGGGAATAGTAGCTGTCAAATGGCCTTCCCTTCCAGCCAGTCTCTGTAC       c.1620
 S  P  V  N  G  N  S  S  C  Q  M  A  F  P  S  S  Q  S  L  Y         p.540

          .         .         .         .                           g.1662
 CGCACGTCCGGAGCTTTCGTCTACGACTGTAGCAAGTTTTGA                         c.1662
 R  T  S  G  A  F  V  Y  D  C  S  K  F  X                           p.553

          .         .         .         .         .         .       g.1722
 cacaccctcaaagccgaactaaatcgaaccccaaagcaggaaaagctaaaggaacccatc       c.*60

          .         .         .         .         .         .       g.1782
 aaggcaaaatcgaaactaaaaaaaaaaaatccaattaaaaaaaacccctgagaatattca       c.*120

          .         .         .         .         .         .       g.1842
 ccacaccagcgaacagaatatccctccaaaaattcagctcaccagcaccagcacgaagaa       c.*180

          .         .         .         .         .         .       g.1902
 aactctattttcttaaccgattaattcagagccacctccactttgccttgtctaaataaa       c.*240

          .         .         .         .         .         .       g.1962
 caaacccgtaaactgttttatacagagacagcaaaatcttggtttattaaaggacagtgt       c.*300

          .         .         .         .         .         .       g.2022
 tactccagataacacgtaagtttcttcttgcttttcagagacctgctttcccctcctccc       c.*360

          .         .         .         .         .         .       g.2082
 gtctcccctctcttgccttcttccttgcctctcacctgtaagatattattttatcctatg       c.*420

          .         .         .         .         .         .       g.2142
 ttgaagggagggggaaagtccccgtttatgaaagtcgctttctttttattcatggacttg       c.*480

          .         .         .         .         .         .       g.2202
 ttttaaaatgtaaattgcaacatagtaatttatttttaatttgtagttggatgtcgtgga       c.*540

          .         .         .         .         .         .       g.2262
 ccaaacgccagaaagtgttcccaaaacctgacgttaaattgcctgaaactttaaattgtg       c.*600

          .         .         .         .         .         .       g.2322
 ctttttttctcattataaaaagggaaactgtattaatcttattctatcctcttttctttc       c.*660

          .         .         .         .         .         .       g.2382
 tttttgttgaacatattcattgtttgtttattaataaattaccattcagtttgaatgaga       c.*720

          .         .         .         .         .         .       g.2442
 cctatatgtctggatactttaatagagctttaattattacgaaaaaagatttcagagata       c.*780

          .         .         .         .         .         .       g.2502
 aaacactagaagttacctattctccacctaaatctctgaaaaatggagaaaccctctgac       c.*840

          .         .         .         .         .         .       g.2562
 tagtccatgtcaaattttactaaaagtctttttgtttagatttattttcctgcagcatct       c.*900

          .         .         .         .         .         .       g.2622
 tctgcaaaatgtactatatagtcagcttgctttgaggctagtaaaaagatatttttctaa       c.*960

          .         .         .         .         .         .       g.2682
 acagattggagttggcatataaacaaatacgttttctcactaatgacagtccatgattcg       c.*1020

          .         .         .         .         .         .       g.2742
 gaaattttaagcccatgaatcagccgcggtcttaccacggtgatgcctgtgtgccgagag       c.*1080

          .         .         .         .         .         .       g.2802
 atgggactgtgcggccagatatgcacagataaatatttggcttgtgtattccatataaaa       c.*1140

          .         .         .         .         .         .       g.2862
 ttgcagtgcatattatacatccctgtgagccagatgctgaatagatattttcctattatt       c.*1200

          .         .         .         .         .         .       g.2922
 tcagtcctttataaaaggaaaaataaaccagtttttaaatgtatgtatataattctcccc       c.*1260

          .         .         .         .         .         .       g.2982
 catttacaatccttcatgtattacatagaaggattgcttttttaaaaatatactgcgggt       c.*1320

          .         .         .         .         .         .       g.3042
 tggaaagggatatttaatctttgagaaactattttagaaaatatgtttgtagaacaatta       c.*1380

          .         .         .         .         .         .       g.3102
 tttttgaaaaagatttaaagcaataacaagaaggaaggcgagaggagcagaacattttgg       c.*1440

          .         .         .         .         .         .       g.3162
 tctagggtggtttctttttaaaccattttttcttgttaatttacagttaaacctagggga       c.*1500

          .         .         .         .         .         .       g.3222
 caatccggattggccctcccccttttgtaaataacccaggaaatgtaataaattcattat       c.*1560

          .         .         .         .         .         .       g.3282
 cttagggtgatctgccctgccaatcagactttggggagatggcgatttgattacagacgt       c.*1620

          .         .         .         .         .         .       g.3342
 tcgggggggtggggggcttgcagtttgttttggagataatacagtttcctgctatctgcc       c.*1680

          .         .         .         .         .         .       g.3402
 gctcctatctagaggcaacacttaagcagtaattgctgttgcttgttgtcaaaatttgat       c.*1740

          .         .         .         .         .                 g.3452
 cattgttaaaggattgctgcaaataaatacactttaatttcagtcaaaaa                 c.*1790

 (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 Forkhead box C1 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.