frataxin (FXN) - coding DNA reference sequence

(used for variant description)

(last modified April 21, 2015)
This file was created to facilitate the description of sequence variants on transcript NM_000144.4 in the FXN gene based on a coding DNA reference sequence following the HGVS recommendations.
The sequence was taken from NG_008845.2, covering FXN transcript NM_000144.4.
Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                     .         .         .         .                g.5040
                     agtctcccttgggtcaggggtcctggttgcactccgtgct       c.-181

 .         .         .         .         .         .                g.5100
 ttgcacaaagcaggctctccatttttgttaaatgcacgaatagtgctaagctgggaagtt       c.-121

 .         .         .         .         .         .                g.5160
 cttcctgaggtctaacctctagctgctcccccacagaagagtgcctgcggccagtggcca       c.-61

 .         .         .         .         .         .                g.5220
 ccaggggtcgccgcagcacccagcgctggagggcggagcgggcggcagacccggagcagc       c.-1

          .         .         .         .         .         .       g.5280
 ATGTGGACTCTCGGGCGCCGCGCAGTAGCCGGCCTCCTGGCGTCACCCAGCCCAGCCCAG       c.60
 M  W  T  L  G  R  R  A  V  A  G  L  L  A  S  P  S  P  A  Q         p.20

          .         .         .         .         .         .       g.5340
 GCCCAGACCCTCACCCGGGTCCCGCGGCCGGCAGAGTTGGCCCCACTCTGCGGCCGCCGT       c.120
 A  Q  T  L  T  R  V  P  R  P  A  E  L  A  P  L  C  G  R  R         p.40

          .         .         .         .      | 02  .         .    g.15837
 GGCCTGCGCACCGACATCGATGCGACCTGCACGCCCCGCCGCGCA | AGTTCGAACCAACGT    c.180
 G  L  R  T  D  I  D  A  T  C  T  P  R  R  A   | S  S  N  Q  R      p.60

          .         .         .         .         .         .       g.15897
 GGCCTCAACCAGATTTGGAATGTCAAAAAGCAGAGTGTCTATTTGATGAATTTGAGGAAA       c.240
 G  L  N  Q  I  W  N  V  K  K  Q  S  V  Y  L  M  N  L  R  K         p.80

          .         .    | 03    .         .         .         .    g.22614
 TCTGGAACTTTGGGCCACCCAGG | CTCTCTAGATGAGACCACCTATGAAAGACTAGCAGAG    c.300
 S  G  T  L  G  H  P  G  |  S  L  D  E  T  T  Y  E  R  L  A  E      p.100

          .         .         .         .         .         .       g.22674
 GAAACGCTGGACTCTTTAGCAGAGTTTTTTGAAGACCTTGCAGACAAGCCATACACGTTT       c.360
 E  T  L  D  S  L  A  E  F  F  E  D  L  A  D  K  P  Y  T  F         p.120

          .         .     | 04   .         .         .         .    g.34411
 GAGGACTATGATGTCTCCTTTGGG | AGTGGTGTCTTAACTGTCAAACTGGGTGGAGATCTA    c.420
 E  D  Y  D  V  S  F  G   | S  G  V  L  T  V  K  L  G  G  D  L      p.140

          .         .         .         .         .         .       g.34471
 GGAACCTATGTGATCAACAAGCAGACGCCAAACAAGCAAATCTGGCTATCTTCTCCATCC       c.480
 G  T  Y  V  I  N  K  Q  T  P  N  K  Q  I  W  L  S  S  P  S         p.160

    | 05     .         .         .         .         .         .    g.42107
 AG | TGGACCTAAGCGTTATGACTGGACTGGGAAAAACTGGGTGTACTCCCACGACGGCGTG    c.540
 S  |  G  P  K  R  Y  D  W  T  G  K  N  W  V  Y  S  H  D  G  V      p.180

          .         .         .         .         .         .       g.42167
 TCCCTCCATGAGCTGCTGGCCGCAGAGCTCACTAAAGCCTTAAAAACCAAACTGGACTTG       c.600
 S  L  H  E  L  L  A  A  E  L  T  K  A  L  K  T  K  L  D  L         p.200

          .         .         .                                     g.42200
 TCTTCCTTGGCCTATTCCGGAAAAGATGCTTGA                                  c.633
 S  S  L  A  Y  S  G  K  D  A  X                                    p.210

          .         .         .         .         .         .       g.42260
 tgcccagccccgttttaaggacattaaaagctatcaggccaagaccccagcttcattatg       c.*60

          .         .         .         .         .         .       g.42320
 cagctgaggtctgttttttgttgttgttgttgtttattttttttattcctgcttttgagg       c.*120

          .         .         .         .         .         .       g.42380
 acagttgggctatgtgtcacagctctgtagaaagaatgtgttgcctcctaccttgccccc       c.*180

          .         .         .         .         .         .       g.42440
 aagttctgatttttaatttctatggaagattttttggattgtcggatttcctccctcaca       c.*240

          .         .         .         .         .         .       g.42500
 tgataccccttatcttttataatgtcttatgcctatacctgaatataacaacctttaaaa       c.*300

          .         .         .         .         .         .       g.42560
 aagcaaaataataagaaggaaaaattccaggagggaaaatgaattgtcttcactcttcat       c.*360

          .         .         .         .         .         .       g.42620
 tctttgaaggatttactgcaagaagtacatgaagagcagctggtcaacctgctcactgtt       c.*420

          .         .         .         .         .         .       g.42680
 ctatctccaaatgagacacattaaagggtagcctacaaatgttttcaggcttctttcaaa       c.*480

          .         .         .         .         .         .       g.42740
 gtgtaagcacttctgagctctttagcattgaagtgtcgaaagcaactcacacgggaagat       c.*540

          .         .         .         .         .         .       g.42800
 catttcttatttgtgctctgtgactgccaaggtgtggcctgcactgggttgtccagggag       c.*600

          .         .         .         .         .         .       g.42860
 acctagtgctgtttctcccacatattcacatacgtgtctgtgtgtatatatattttttca       c.*660

          .         .         .         .         .         .       g.42920
 atttaaaggttagtatggaatcagctgctacaagaatgcaaaaaatcttccaaagacaag       c.*720

          .         .         .         .         .         .       g.42980
 aaaagaggaaaaaaagccgttttcatgagctgagtgatgtagcgtaacaaacaaaatcat       c.*780

          .         .         .         .         .         .       g.43040
 ggagctgaggaggtgccttgtaaacatgaaggggcagataaaggaaggagatactcatgt       c.*840

          .         .         .         .         .         .       g.43100
 tgataaagagagccctggtcctagacatagttcagccacaaagtagttgtccctttgtgg       c.*900

          .         .         .         .         .         .       g.43160
 acaagtttcccaaattccctggacctctgcttccccatctgttaaatgagagaatagagt       c.*960

          .         .         .         .         .         .       g.43220
 atggttgattcccagcattcagtggtcctgtcaagcaacctaacaggctagttctaattc       c.*1020

          .         .         .         .         .         .       g.43280
 cctattgggtagatgaggggatgacaaagaacagtttttaagctatataggaaacattgt       c.*1080

          .         .         .         .         .         .       g.43340
 tattggtgttgccctatcgtgatttcagttgaattcatgtgaaaataatagccatccttg       c.*1140

          .         .         .         .         .         .       g.43400
 gcctggcgcggtggctcacacctgtaatcccagcacttttggaggccaaggtgggtggat       c.*1200

          .         .         .         .         .         .       g.43460
 cacctgaggtcaggagttcaagaccagcctggccaacatgatgaaaccccgtctctacta       c.*1260

          .         .         .         .         .         .       g.43520
 aaaatacaaaaaattagccgggcatgatggcaggtgcctgtaatcccagctacttgggag       c.*1320

          .         .         .         .         .         .       g.43580
 gctgaagcggaagaatcgcttgaacccagaggtggaggttgcagtgagccgagatcgtgc       c.*1380

          .         .         .         .         .         .       g.43640
 cattgcactgtaacctgggtgactgagcaaaactctgtctcaaaataataataacaatat       c.*1440

          .         .         .         .         .         .       g.43700
 aataataataatagccatcctttattgtacccttactgggttaatcgtattataccacat       c.*1500

          .         .         .         .         .         .       g.43760
 tacctcattttaatttttactgacctgcactttatacaaagcaacaagcctccaggacat       c.*1560

          .         .         .         .         .         .       g.43820
 taaaattcatgcaaagttatgctcatgttatattattttcttacttaaagaaggatttat       c.*1620

          .         .         .         .         .         .       g.43880
 tagtggctgggcatggtggcgtgcacctgtaatcccaggtactcaggaggctgagacggg       c.*1680

          .         .         .         .         .         .       g.43940
 agaattgcttgaccccaggcggaggaggttacagtgagtcgagatcgtacctgagcgaca       c.*1740

          .         .         .         .         .         .       g.44000
 gagcgagactccgtctcaaaaaaaaaaaaaaggagggtttattaatgagaagtttgtatt       c.*1800

          .         .         .         .         .         .       g.44060
 aatatgtagcaaaggcttttccaatgggtgaataaaaacacattccattaagtcaagctg       c.*1860

          .         .         .         .         .         .       g.44120
 ggagcagtggcatatacctatagtcccagctgcacaggaggctgagacaggaggattgct       c.*1920

          .         .         .         .         .         .       g.44180
 tgaagccaggaattggagatcagcctgggcaacacagcaagatcctatctcttaaaaaaa       c.*1980

          .         .         .         .         .         .       g.44240
 gaaaaaaaaacctattaataataaaacagtataaacaaaagctaaataggtaaaatattt       c.*2040

          .         .         .         .         .         .       g.44300
 tttctgaaataaaattattttttgagtctgatggaaatgtttaagtgcagtaggccagtg       c.*2100

          .         .         .         .         .         .       g.44360
 ccagtgagaaaataaataacatcatacatgtttgtatgtgtttgcatcttgcttctactg       c.*2160

          .         .         .         .         .         .       g.44420
 aaagtttcagtgcaccccacttacttagaactcggtgacatgatgtactcctttatctgg       c.*2220

          .         .         .         .         .         .       g.44480
 gacacagcacaaaagaggtatgcagtggggctgctctgacatgaaagtggaagttaagga       c.*2280

          .         .         .         .         .         .       g.44540
 atctgggctcttatggggtccttgtgggccagcccttcaggcctattttactttcatttt       c.*2340

          .         .         .         .         .         .       g.44600
 acatatagctctaattggtttgattatctcgttcccaaggcagtgggagatccccattta       c.*2400

          .         .         .         .         .         .       g.44660
 aggaaagaaaaggggcctggcacagtggctcatgcctgtaatcccagcactttgggaggc       c.*2460

          .         .         .         .         .         .       g.44720
 tgaggcaagtgtatcacctgaggtcaggagttcaagaccagcctggccaacatggcaaaa       c.*2520

          .         .         .         .         .         .       g.44780
 tcccgtctctactaaaaatattaaaaaattggctgggcgtggtggttcgtgcctataatt       c.*2580

          .         .         .         .         .         .       g.44840
 tcagctactcaggaggctgaggcaggagaatcgctgtaacctggggggtggaggttgcag       c.*2640

          .         .         .         .         .         .       g.44900
 tgagacgagatcatgccacttcactccagcctggccaacagagccatactccgtctcaaa       c.*2700

          .         .         .         .         .         .       g.44960
 taaataaataaataaataaagggacttcaaacacatgaacagcagccaggggaagaatca       c.*2760

          .         .         .         .         .         .       g.45020
 aaatcatattctgtcaagcaaactggaaaagtaccactgtgtgtaccaatagcctcccca       c.*2820

          .         .         .         .         .         .       g.45080
 ccacagaccctgggagcatcgcctcatttatggtgtggtccagtcatccatgtgaaggat       c.*2880

          .         .         .         .         .         .       g.45140
 gagtttccaggaaaaggttattaaatattcactgtaacatactggaggaggtgaggaatt       c.*2940

          .         .         .         .         .         .       g.45200
 gcataatacaatcttagaaaacttttttttcccctttctattttttgagacaggatctca       c.*3000

          .         .         .         .         .         .       g.45260
 ctttggcactcaggctggaggacagtggtacaatcaaagctcatggcagcctcgacctcc       c.*3060

          .         .         .         .         .         .       g.45320
 ctgggcttgggcaatcctcccacaggtgtgcacctccatagctggctaatttgtgtattt       c.*3120

          .         .         .         .         .         .       g.45380
 tttgtagagatggggtttcaccatgttgcccaggctggtctctaacacttaggctcaagt       c.*3180

          .         .         .         .         .         .       g.45440
 gatccacctgcctcgtcctcccaagatgctgggattacaggtgtgtgccacaggtgttca       c.*3240

          .         .         .         .         .         .       g.45500
 tcagaaagctttttctattatttttaccttcttgagtgggtagaacctcagccacataga       c.*3300

          .         .         .         .         .         .       g.45560
 aaataaaatgttctggcatgacttatttagctctctggaattacaaagaaggaatgaggt       c.*3360

          .         .         .         .         .         .       g.45620
 gtgtaaaagagaacctgggtttttgaatcacaaatttagaatttaatcgaaactctgcct       c.*3420

          .         .         .         .         .         .       g.45680
 cttacttgtttgtagacactgacagtggcctcatgttttttttttttttaatctataaaa       c.*3480

          .         .         .         .         .         .       g.45740
 tggagatatctaacatgttgagcctgggcccacaggcaaagcacaatcctgatgtgagaa       c.*3540

          .         .         .         .         .         .       g.45800
 gtactcagttcatgacaactgttgttctcacatgcatagcataatttcatattcacattg       c.*3600

          .         .         .         .         .         .       g.45860
 gaggacttctcccaaaatatggatgacgttccctactcaaccttgaacttaatcaaaata       c.*3660

          .         .         .         .         .         .       g.45920
 ctcagtttacttaacttcgtattagattctgattccctggaaccatttatcgtgtgcctt       c.*3720

          .         .         .         .         .         .       g.45980
 accatgcttatattttacttgatcttttgcataccttctaaaactattttagccaattta       c.*3780

          .         .         .         .         .         .       g.46040
 aaatttgacagtttgcattaaattataggtttacaatatgctttatccagctatacctgc       c.*3840

          .         .         .         .         .         .       g.46100
 cccaaattctgacagatgcttttgccacctctaaaggaagacccatgttcatagtgatgg       c.*3900

          .         .         .         .         .         .       g.46160
 agtttgtgtggactaaccatgcaaggttgccaaggaaaaatcgctttacgcttccaaggt       c.*3960

          .         .         .         .         .         .       g.46220
 acacactaagatgaaagtaattttagtccgtgtccagttggattcttggcacatagttat       c.*4020

          .         .         .         .         .         .       g.46280
 cttctgctagaacaaactaaaacagctacatgccagcaagggagaaaggggaaggagggg       c.*4080

          .         .         .         .         .         .       g.46340
 caaagttttgaaatttcatgtaaatttatgctgttcaaaacgacgagttcatgactttgt       c.*4140

          .         .         .         .         .         .       g.46400
 gtatagagtaagaaatgccttttcttttttgagacagagtcttgctctgtcacccaggct       c.*4200

          .         .         .         .         .         .       g.46460
 ggagtgcagtggcacgatctgggctcactacaacctccgcctcctgggttcaagcaattc       c.*4260

          .         .         .         .         .         .       g.46520
 tctgcctcagcctcccgagtagctgggattacaggtgcctgccaccacacccggctaatt       c.*4320

          .         .         .         .         .         .       g.46580
 tttgtatttttagtagagacggggtttcaccatcatggccaggctggtcttgaactcctg       c.*4380

          .         .         .         .         .         .       g.46640
 acctagtaatccacctgcctccgcctcccaaagtgctgggattacaggcgtgagccactg       c.*4440

          .         .         .         .         .         .       g.46700
 cacccagccagaaatgccttctaatctttggtttatcttaattagccaggacacttggag       c.*4500

          .         .         .         .         .         .       g.46760
 tgcatcccgaagtacctgatcagtggcccctttggaatgtgtaaaactcagctcacttat       c.*4560

          .         .         .         .         .         .       g.46820
 atccctgcatccgctacagagacagaatccaagctcatatgttccatcttctctggctgt       c.*4620

          .         .         .         .         .         .       g.46880
 atagtttaaggaatggaaggcaccagaacagatttattgaaatgtttattagctgaagat       c.*4680

          .         .         .         .         .         .       g.46940
 ttatttagacagttgaggaaaacatcagcacccagcagtaaaattggctctcaaagattt       c.*4740

          .         .         .         .         .         .       g.47000
 tcttctcctgtggaaagtcagacctctgaggccccatccaggtagaagtactagtgcaag       c.*4800

          .         .         .         .         .         .       g.47060
 aagggcctctgctgtccacttgtgtttctgtgatctgtgggaacattgttaacgccacat       c.*4860

          .         .         .         .         .         .       g.47120
 cttgacctcaaattgtttagctcctggccagacacggtggctcacacctgtaatcccagc       c.*4920

          .         .         .         .         .         .       g.47180
 actttgagaggctgaggcaggtggatcacctgaggttaggagttcgaggccagcctggtc       c.*4980

          .         .         .         .         .         .       g.47240
 aacatggtaaaaccccgcctctactaaaaatacaaaaattagctggccgtagtggcgcac       c.*5040

          .         .         .         .         .         .       g.47300
 gcctgttatcccagctactcgggaggctgaggcaggagaattgcttgaacctgggtggtg       c.*5100

          .         .         .         .         .         .       g.47360
 gaggttgcagtgagccgagattacaccactgcactccagcctgggtgacaagagggaaac       c.*5160

          .         .         .         .         .         .       g.47420
 tccattaaaaaaatgtaattcccgtgtctgccatcttaagtgtaaaggtggctaaattat       c.*5220

          .         .         .         .         .         .       g.47480
 atagaaaaataagacaatatcatttcccaattacattcctttcctaccgcactctatgat       c.*5280

          .         .         .         .         .         .       g.47540
 gctagctgagatttttccaaaagaaaatggcttaaataaaaccctaagagaaagaaaaac       c.*5340

          .         .         .         .         .         .       g.47600
 tttaaatccctccaaagctcaaaagtaatagaaacagatgagtttggagtcaggatttct       c.*5400

          .         .         .         .         .         .       g.47660
 ctgtaagattgcctaggctgtgtactgcacatctccaggtgccactgttgacagagatta       c.*5460

          .         .         .         .         .         .       g.47720
 taactacaatgtgaagtgaatggtgccactgacagttatgcaaaccgtccagagcatagc       c.*5520

          .         .         .         .         .         .       g.47780
 cacctgatcctgctgggattcctcttgccagtccatcagcagttccccttgaaagtttca       c.*5580

          .         .         .         .         .         .       g.47840
 ccaaacatcccttaaatctgccctctcctgcccgtccccagtggaggtcctcatcatttt       c.*5640

          .         .         .         .         .         .       g.47900
 tcacctgcatttttgcaggagctttcttatatccaccttcctccttttctctcagcccat       c.*5700

          .         .         .         .         .         .       g.47960
 catctagctacacagtctccagggtaagctttcagaaaggcaatctcttgtctgtaaaac       c.*5760

          .         .         .         .         .         .       g.48020
 ctaagcaggaccaaggccaagtttcttagcctgaaaaatgtgcttttctgactgaactgt       c.*5820

          .         .         .         .         .         .       g.48080
 tcaggcactgactctacatataattatgcttttctaccccctcacactcaacactttgac       c.*5880

          .         .         .         .         .         .       g.48140
 tccagcaatcccaaatccccagatccctaagtgtgctgtgctattttcacgtggctctca       c.*5940

          .         .         .         .         .         .       g.48200
 gacttggccagtgctgtttccattttggtctttattccccacatctctgcctggggggta       c.*6000

          .         .         .         .         .         .       g.48260
 gattctaccctgaaaaatgttcttggcacagccttgcaaactcctcctccactcagcctc       c.*6060

          .         .         .         .         .         .       g.48320
 tgcctggatgcccttgattgttccatgtcctcagcataccatgtttgtctttcccagcac       c.*6120

          .         .         .         .         .         .       g.48380
 tgacctaccatgtgtcacccctgcttggctgtaccttccatgaggctaggactatgtgtc       c.*6180

          .         .         .         .         .         .       g.48440
 tcctttgttgactgctgttgccctagcatcttgcacagttccttgcacacaattagagct       c.*6240

          .         .         .         .         .         .       g.48500
 ctataaatgtcaaataaatgtgttataattatatgtttaagatagttgttcaaataaact       c.*6300

          .                                                         g.48515
 ctaaataaccccaac                                                    c.*6315

 (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 Frataxin 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.