forkhead box G1 (FOXG1) - coding DNA reference sequence

(used for variant description)

(last modified November 2, 2012)

This file was created to facilitate the description of sequence variants on transcript NM_005249.4 in the FOXG1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000014.8, covering FOXG1 transcript NM_005249.4.

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

 (upstream sequence)
                                         .         .                g.5028
                                 taattcctgaggggtggttgctgctttt       c.-181

 .         .         .         .         .         .                g.5088
 gctacatgacttgccagcgcccgagcctgcggtccaactgcgctgctgccggagcgctca       c.-121

 .         .         .         .         .         .                g.5148
 gtgccgccgctgccgcccgcgccccccgcgccccgttcggcacccaccggtcgccgccgc       c.-61

 .         .         .         .         .         .                g.5208
 ccgccgcgccgctgtcccgctcccgcgccgccgccgccgtttccccccgacgactgggtg       c.-1

          .         .         .         .         .         .       g.5268
 ATGCTGGACATGGGAGATAGGAAAGAGGTGAAAATGATCCCCAAGTCCTCGTTCAGCATC       c.60
 M  L  D  M  G  D  R  K  E  V  K  M  I  P  K  S  S  F  S  I         p.20

          .         .         .         .         .         .       g.5328
 AACAGCCTGGTGCCCGAGGCGGTCCAGAACGACAACCACCACGCGAGCCACGGCCACCAC       c.120
 N  S  L  V  P  E  A  V  Q  N  D  N  H  H  A  S  H  G  H  H         p.40

          .         .         .         .         .         .       g.5388
 AACAGCCACCACCCCCAGCACCACCACCACCACCACCACCATCACCACCACCCGCCGCCG       c.180
 N  S  H  H  P  Q  H  H  H  H  H  H  H  H  H  H  H  P  P  P         p.60

          .         .         .         .         .         .       g.5448
 CCCGCCCCGCAACCGCCGCCGCCGCCGCAGCAGCAGCAGCCGCCGCCGCCGCCGCCCCCG       c.240
 P  A  P  Q  P  P  P  P  P  Q  Q  Q  Q  P  P  P  P  P  P  P         p.80

          .         .         .         .         .         .       g.5508
 GCACCGCAGCCCCCCCAGACGCGGGGCGCCCCGGCCGCCGACGACGACAAGGGCCCCCAG       c.300
 A  P  Q  P  P  Q  T  R  G  A  P  A  A  D  D  D  K  G  P  Q         p.100

          .         .         .         .         .         .       g.5568
 CAGCTGCTGCTCCCGCCGCCGCCACCGCCACCACCGGCCGCCGCCCTGGACGGGGCTAAA       c.360
 Q  L  L  L  P  P  P  P  P  P  P  P  A  A  A  L  D  G  A  K         p.120

          .         .         .         .         .         .       g.5628
 GCGGACGGGCTGGGCGGCAAGGGCGAGCCGGGCGGCGGGCCGGGGGAGCTGGCGCCCGTC       c.420
 A  D  G  L  G  G  K  G  E  P  G  G  G  P  G  E  L  A  P  V         p.140

          .         .         .         .         .         .       g.5688
 GGGCCGGACGAGAAGGAGAAGGGCGCCGGCGCCGGGGGGGAGGAGAAGAAGGGGGCGGGC       c.480
 G  P  D  E  K  E  K  G  A  G  A  G  G  E  E  K  K  G  A  G         p.160

          .         .         .         .         .         .       g.5748
 GAGGGCGGCAAGGACGGGGAGGGGGGCAAGGAGGGCGAGAAGAAGAACGGCAAGTACGAG       c.540
 E  G  G  K  D  G  E  G  G  K  E  G  E  K  K  N  G  K  Y  E         p.180

          .         .         .         .         .         .       g.5808
 AAGCCGCCGTTCAGCTACAACGCGCTCATCATGATGGCCATCCGGCAGAGCCCCGAGAAG       c.600
 K  P  P  F  S  Y  N  A  L  I  M  M  A  I  R  Q  S  P  E  K         p.200

          .         .         .         .         .         .       g.5868
 CGGCTCACGCTCAACGGCATCTACGAGTTCATCATGAAGAACTTCCCTTACTACCGCGAG       c.660
 R  L  T  L  N  G  I  Y  E  F  I  M  K  N  F  P  Y  Y  R  E         p.220

          .         .         .         .         .         .       g.5928
 AACAAGCAGGGCTGGCAGAACTCCATCCGCCACAATCTGTCCCTCAACAAGTGCTTCGTG       c.720
 N  K  Q  G  W  Q  N  S  I  R  H  N  L  S  L  N  K  C  F  V         p.240

          .         .         .         .         .         .       g.5988
 AAGGTGCCGCGCCACTACGACGACCCGGGCAAGGGCAACTACTGGATGCTGGACCCGTCG       c.780
 K  V  P  R  H  Y  D  D  P  G  K  G  N  Y  W  M  L  D  P  S         p.260

          .         .         .         .         .         .       g.6048
 AGCGACGACGTGTTCATCGGCGGCACCACGGGCAAGCTGCGGCGCCGCTCCACCACCTCG       c.840
 S  D  D  V  F  I  G  G  T  T  G  K  L  R  R  R  S  T  T  S         p.280

          .         .         .         .         .         .       g.6108
 CGGGCCAAGCTGGCCTTCAAGCGCGGTGCGCGCCTCACCTCCACCGGCCTCACCTTCATG       c.900
 R  A  K  L  A  F  K  R  G  A  R  L  T  S  T  G  L  T  F  M         p.300

          .         .         .         .         .         .       g.6168
 GACCGCGCCGGCTCCCTCTACTGGCCCATGTCGCCCTTCCTGTCCCTGCACCACCCCCGC       c.960
 D  R  A  G  S  L  Y  W  P  M  S  P  F  L  S  L  H  H  P  R         p.320

          .         .         .         .         .         .       g.6228
 GCCAGCAGCACTTTGAGTTACAACGGCACCACGTCGGCCTACCCCAGCCACCCCATGCCC       c.1020
 A  S  S  T  L  S  Y  N  G  T  T  S  A  Y  P  S  H  P  M  P         p.340

          .         .         .         .         .         .       g.6288
 TACAGCTCCGTGTTGACTCAGAACTCGCTGGGCAACAACCACTCCTTCTCCACCGCCAAC       c.1080
 Y  S  S  V  L  T  Q  N  S  L  G  N  N  H  S  F  S  T  A  N         p.360

          .         .         .         .         .         .       g.6348
 GGCCTGAGCGTGGACCGGCTGGTCAACGGGGAGATCCCGTACGCCACGCACCACCTCACG       c.1140
 G  L  S  V  D  R  L  V  N  G  E  I  P  Y  A  T  H  H  L  T         p.380

          .         .         .         .         .         .       g.6408
 GCCGCCGCGCTAGCCGCCTCGGTGCCCTGCGGCCTGTCGGTGCCCTGCTCTGGGACCTAC       c.1200
 A  A  A  L  A  A  S  V  P  C  G  L  S  V  P  C  S  G  T  Y         p.400

          .         .         .         .         .         .       g.6468
 TCCCTCAACCCCTGCTCCGTCAACCTGCTCGCGGGCCAGACCAGTTACTTTTTCCCCCAC       c.1260
 S  L  N  P  C  S  V  N  L  L  A  G  Q  T  S  Y  F  F  P  H         p.420

          .         .         .         .         .         .       g.6528
 GTCCCGCACCCGTCAATGACTTCGCAGAGCAGCACGTCCATGAGCGCCAGGGCCGCGTCC       c.1320
 V  P  H  P  S  M  T  S  Q  S  S  T  S  M  S  A  R  A  A  S         p.440

          .         .         .         .         .         .       g.6588
 TCCTCCACGTCGCCGCAGGCCCCCTCGACCCTGCCCTGTGAGTCTTTAAGACCCTCTTTG       c.1380
 S  S  T  S  P  Q  A  P  S  T  L  P  C  E  S  L  R  P  S  L         p.460

          .         .         .         .         .         .       g.6648
 CCAAGTTTTACGACGGGACTGTCTGGGGGACTGTCTGATTATTTCACACATCAAAATCAG       c.1440
 P  S  F  T  T  G  L  S  G  G  L  S  D  Y  F  T  H  Q  N  Q         p.480

          .         .         .                                     g.6678
 GGGTCTTCTTCCAACCCTTTAATACATTAA                                     c.1470
 G  S  S  S  N  P  L  I  H  X                                       p.489

          .         .         .         .         .         .       g.6738
 catccctgggaccagactgtaagtgaacgttttacacacatttgcattgtaaatgataat       c.*60

          .         .         .         .         .         .       g.6798
 taaaaaaataagtccaggtattttttattaagcccccccctcccatttctgtacgtttgt       c.*120

          .         .         .         .         .         .       g.6858
 tcagtctctagggttgtttattattctaacaaggtgtggagtgtcagcgaggtgcaatgt       c.*180

          .         .         .         .         .         .       g.6918
 ggggagaatacattgtagaatataaggtttggaagtcaaattatagtagaatgtgtatct       c.*240

          .         .         .         .         .         .       g.6978
 aaatagtgactgctttgccatttcattcaaacctgacaagtctatctctaagagccgcca       c.*300

          .         .         .         .         .         .       g.7038
 gatttccatgtgtgcagtattataagttatcatggaactatatggtggacgcagaccttg       c.*360

          .         .         .         .         .         .       g.7098
 agaacaacctaaattatggggagaattttaaaatgttaaactgtaatttgtatttaaaaa       c.*420

          .         .         .         .         .         .       g.7158
 gcattcgtagtaaaggtgcccaagaaattattttggccatttattgttttgtccttttct       c.*480

          .         .         .         .         .         .       g.7218
 ttaaagaactgtttttttttcttttgtttacttttagaccaaagattgggttctagaaaa       c.*540

          .         .         .         .         .         .       g.7278
 tgcacttggtatactaagtattaaaacaaacaaaaaggaaagttgtttcagttggcaaca       c.*600

          .         .         .         .         .         .       g.7338
 ctgcccattcaattgaatcagaaggggacaaaattaacgattgccttcagtttgtgttgt       c.*660

          .         .         .         .         .         .       g.7398
 gtatattttgatgtatgtggtcactaacaggtcacttttattttttctaaatgtagtgaa       c.*720

          .         .         .         .         .         .       g.7458
 atgttaatacctattgtacttataggtaaaccttgcaaatatgtaacctgtgttgcgcaa       c.*780

          .         .         .         .         .         .       g.7518
 atgccgcataaatttgagtgattgttaatgttgtcttaaaatttcttgattgtgatactg       c.*840

          .         .         .         .         .         .       g.7578
 tggtcatatgcccgtgtttgtcacttacaaaaatgtttactatgaacacacagaaataaa       c.*900

          .         .         .         .         .         .       g.7638
 aaataggctaaattcatatatatcttgatacttttgtctcttttattaagtagagctaat       c.*960

          .         .         .         .         .         .       g.7698
 tttttaaagaccaatcaacttatagggaattcaaaggctttttcagccaaactaaaattt       c.*1020

          .         .         .         .         .         .       g.7758
 aaactgctcctttaatttgaactgactctaaaaatgaaaatagtatttttccctttgtga       c.*1080

          .         .         .         .         .         .       g.7818
 acaaattttacaaggagcagcctatttaataaacactagctttaaacaaagtataggctt       c.*1140

          .         .         .         .         .         .       g.7878
 ttcagctgatacctgtaagtttctgtggatatacagcaaaaagagatataatttaatttt       c.*1200

          .         .         .         .         .         .       g.7938
 ctgtgcatagctctttaccctgtgtttatttccaaatccattaatagaatgccatttata       c.*1260

          .         .         .         .         .         .       g.7998
 tattttgtttcaggtatattgttaatagagcttggcaaattataaataaatatatgtata       c.*1320

          .         .         .         .         .         .       g.8058
 tggttagatagaagtgactataatgcacacatatgtaatatatatagacacacagagccc       c.*1380

          .         .         .         .         .         .       g.8118
 ttcagttcaggtacaatttgcgctatgaatgctgcaaacatttttgtttaaatatttgta       c.*1440

          .         .         .         .         .         .       g.8178
 tttatactttctaagtcagcatttatttttgtggctgtttacccacaatgaaagagttct       c.*1500

          .         .                                               g.8206
 aataaagatgtgctgaagttgcaatata                                       c.*1528

 (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 G1 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.