Polymerase I and Transcript Release Factor (cavin-1) (PTRF) - coding DNA reference sequence

(used for mutation description)

(last modified December 19, 2009)

This file was created to facilitate the description of sequence variants in the PTRF gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_015845.1, covering PTRF transcript NM_012232.5.

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

 (upstream sequence)
                     .         .         .         .                g.5043
                  aatcagcgatcagactccggagtttggcccgggagctggggag       c.-181

 .         .         .         .         .         .                g.5103
 ctcaccgatcccccgcccagcagttctggccgctgtcccggtgcgcacggacgtggctcg       c.-121

 .         .         .         .         .         .                g.5163
 agtttcctctgctctccgctctcgcccgctagctctcctcccttccgctcctgcttctct       c.-61

 .         .         .         .         .         .                g.5223
 ccgggtctcccgctccagctccagccccacccggccggtcccgcacggctccgggtagcc       c.-1

          .         .         .         .         .         .       g.5283
 ATGGAGGACCCCACGCTCTATATTGTCGAGCGGCCGCTTCCCGGGTACCCCGACGCCGAG       c.60
 M  E  D  P  T  L  Y  I  V  E  R  P  L  P  G  Y  P  D  A  E         p.20

          .         .         .         .         .         .       g.5343
 GCCCCGGAGCCTTCCTCCGCTGGGGCTCAGGCAGCGGAGGAGCCGTCGGGGGCCGGCTCA       c.120
 A  P  E  P  S  S  A  G  A  Q  A  A  E  E  P  S  G  A  G  S         p.40

          .         .         .         .         .         .       g.5403
 GAAGAGCTGATCAAGTCGGACCAGGTGAACGGCGTGCTGGTGCTGAGCCTCCTGGACAAA       c.180
 E  E  L  I  K  S  D  Q  V  N  G  V  L  V  L  S  L  L  D  K         p.60

          .         .         .         .         .         .       g.5463
 ATCATCGGGGCCGTAGACCAGATCCAGCTGACTCAAGCACAGCTGGAGGAGCGGCAGGCG       c.240
 I  I  G  A  V  D  Q  I  Q  L  T  Q  A  Q  L  E  E  R  Q  A         p.80

          .         .         .         .         .         .       g.5523
 GAGATGGAGGGCGCAGTGCAGAGCATCCAGGGCGAGCTGAGCAAGCTGGGCAAGGCGCAC       c.300
 E  M  E  G  A  V  Q  S  I  Q  G  E  L  S  K  L  G  K  A  H         p.100

          .         .         .         .         .         .       g.5583
 GCCACCACGAGCAATACGGTGAGCAAGCTGCTGGAGAAGGTGCGCAAGGTCAGCGTCAAC       c.360
 A  T  T  S  N  T  V  S  K  L  L  E  K  V  R  K  V  S  V  N         p.120

          .         .         .         .         .         .       g.5643
 GTGAAGACCGTGCGCGGCAGCCTGGAGCGCCAGGCGGGGCAGATCAAGAAGCTGGAGGTC       c.420
 V  K  T  V  R  G  S  L  E  R  Q  A  G  Q  I  K  K  L  E  V         p.140

          .         .         .         .         .  | 02      .    g.22941
 AACGAGGCCGAGCTGCTGCGGCGCCGCAACTTTAAAGTCATGATCTACCAG | GATGAAGTG    c.480
 N  E  A  E  L  L  R  R  R  N  F  K  V  M  I  Y  Q   | D  E  V      p.160

          .         .         .         .         .         .       g.23001
 AAGCTGCCGGCCAAACTGAGCATCAGCAAATCGCTGAAAGAGTCGGAGGCGCTGCCAGAG       c.540
 K  L  P  A  K  L  S  I  S  K  S  L  K  E  S  E  A  L  P  E         p.180

          .         .         .         .         .         .       g.23061
 AAGGAGGGCGAGGAGCTGGGCGAGGGCGAGCGGCCCGAGGAGGACGCAGCGGCGCTGGAG       c.600
 K  E  G  E  E  L  G  E  G  E  R  P  E  E  D  A  A  A  L  E         p.200

          .         .         .         .         .         .       g.23121
 CTTTCGTCGGACGAGGCGGTGGAGGTTGAGGAGGTTATTGAGGAGTCCCGCGCAGAGCGT       c.660
 L  S  S  D  E  A  V  E  V  E  E  V  I  E  E  S  R  A  E  R         p.220

          .         .         .         .         .         .       g.23181
 ATCAAGCGCAGCGGCCTGCGGCGCGTGGACGACTTCAAGAAGGCCTTCTCCAAGGAGAAG       c.720
 I  K  R  S  G  L  R  R  V  D  D  F  K  K  A  F  S  K  E  K         p.240

          .         .         .         .         .         .       g.23241
 ATGGAGAAGACCAAGGTGCGTACCCGCGAGAACCTGGAGAAGACGCGCCTCAAGACCAAG       c.780
 M  E  K  T  K  V  R  T  R  E  N  L  E  K  T  R  L  K  T  K         p.260

          .         .         .         .         .         .       g.23301
 GAAAACCTGGAGAAGACGCGGCACACCCTGGAGAAGCGCATGAACAAGCTGGGCACGCGC       c.840
 E  N  L  E  K  T  R  H  T  L  E  K  R  M  N  K  L  G  T  R         p.280

          .         .         .         .         .         .       g.23361
 CTGGTGCCCGCCGAGCGGCGCGAGAAACTGAAGACGTCGCGGGACAAGTTGCGCAAATCC       c.900
 L  V  P  A  E  R  R  E  K  L  K  T  S  R  D  K  L  R  K  S         p.300

          .         .         .         .         .         .       g.23421
 TTCACGCCCGACCACGTGGTGTACGCGCGCTCCAAGACCGCGGTCTACAAGGTGCCACCC       c.960
 F  T  P  D  H  V  V  Y  A  R  S  K  T  A  V  Y  K  V  P  P         p.320

          .         .         .         .         .         .       g.23481
 TTCACCTTCCACGTCAAGAAGATCCGCGAGGGCCAGGTGGAAGTGCTCAAGGCCACCGAG       c.1020
 F  T  F  H  V  K  K  I  R  E  G  Q  V  E  V  L  K  A  T  E         p.340

          .         .         .         .         .         .       g.23541
 ATGGTGGAGGTGGGCGCCGACGACGACGAGGGCGGCGCGGAGCGCGGGGAGGCCGGCGAC       c.1080
 M  V  E  V  G  A  D  D  D  E  G  G  A  E  R  G  E  A  G  D         p.360

          .         .         .         .         .         .       g.23601
 CTGCGGCGCGGGAGCAGCCCCGACGTGCACGCGCTGCTGGAGATCACCGAGGAGTCGGAC       c.1140
 L  R  R  G  S  S  P  D  V  H  A  L  L  E  I  T  E  E  S  D         p.380

          .         .         .                                     g.23634
 GCCGTGCTGGTGGACAAGAGCGACAGCGACTGA                                  c.1173
 A  V  L  V  D  K  S  D  S  D  X                                    p.390

          .         .         .         .         .         .       g.23694
 gccgcccccgctgccacccaccccattcctcgctccttccgaacttcctctttcgcattc       c.*60

          .         .         .         .         .         .       g.23754
 tctctcggctcgagctggctgagatttttctaaattgaaaacacgcccccctccccacac       c.*120

          .         .         .         .         .         .       g.23814
 ctccaggaactccactcccagtcttagagctgttaggacccgatggggaggcagcccccg       c.*180

          .         .         .         .         .         .       g.23874
 cagtggacaacccccgcttggacacagtccgagtggaatgggaagggaatggtcaatccc       c.*240

          .         .         .         .         .         .       g.23934
 tgtcctggttgtccaagtcgggatctcagaggaaattgcagtgattccacggttaggccc       c.*300

          .         .         .         .         .         .       g.23994
 ccctgggggggctgccttcccctcagcctctccccacaccacccacccagctgctgtcat       c.*360

          .         .         .         .         .         .       g.24054
 tccgctcactgagctcttcttcattctcaccctgatccctgggggactcaaagccaaaac       c.*420

          .         .         .         .         .         .       g.24114
 tgcccaaagaggaaagattgaatcctaaaggggatccctgcccccatgggaggcccccta       c.*480

          .         .         .         .         .         .       g.24174
 ctagaaggacgtgaaagcagcttttgggggaaactgaggcagtggggaagacagagcaga       c.*540

          .         .         .         .         .         .       g.24234
 atgagccctcaccctggctgggggtccagcacaggctgtatctgcagagggtcccagagg       c.*600

          .         .         .         .         .         .       g.24294
 aacgctggagccaagagaagccctgggaaggaggggtggggaacgacatgcatgtgaggg       c.*660

          .         .         .         .         .         .       g.24354
 atggcacactgatgtgtttatgcacctgtacacaggagcgcatggccatggctttggaaa       c.*720

          .         .         .         .         .         .       g.24414
 ggagaatggaaaaatagaagaaggtcggccgggcttggtggcttatgcctgtaaccccag       c.*780

          .         .         .         .         .         .       g.24474
 cactttgggaggccgaggtgggcggatcacctgaagtcaggagttcgggaccagcctggc       c.*840

          .         .         .         .         .         .       g.24534
 aaacaccccatctctactaagcgaaaacccatctctactaaaattacaaaaattagctgg       c.*900

          .         .         .         .         .         .       g.24594
 gcatggttgcgcatgcctgtaatcccagctactttggaggctgaggtggggagaattgct       c.*960

          .         .         .         .         .         .       g.24654
 tgaacctgggaggtggaggttgcagtgagccaaggtcgcgacactgcactccagcctggg       c.*1020

          .         .         .         .         .         .       g.24714
 tgacagagtgagactccatctcaacagaaggaaaaaaaaggaaaataggagaaggtggaa       c.*1080

          .         .         .         .         .         .       g.24774
 atgggtgaagagagaagtcccctcactagctgcatgagaaatctatcttactgtggttct       c.*1140

          .         .         .         .         .         .       g.24834
 ccatgggcagcaggaccatttttcagaatcaagagggaggacagtgtgagaaggcgatga       c.*1200

          .         .         .         .         .         .       g.24894
 tccaaagaagacagagaggtcagccccacccgatccctcaaatgggctcttggaggcacc       c.*1260

          .         .         .         .         .         .       g.24954
 cccaggggcagcccatttctcaaagtccagaaaattagggtcccagaagggggcagcagc       c.*1320

          .         .         .         .         .         .       g.25014
 aggctgggagttaggagggagagcagggtgccggccctgccaccaagttgagagctggag       c.*1380

          .         .         .         .         .         .       g.25074
 gggaggtggggagagaacatcacagagcagccagccctggttcactcctggcagtttctt       c.*1440

          .         .         .         .         .         .       g.25134
 ctcaagctccttccctaggagcatggtggcacgtgcctgtggtctcagctacttgggagg       c.*1500

          .         .         .         .         .         .       g.25194
 ctgaggcgggaggatcgccagagcccaggagtttgaggctgcagtgagctatgagggtgc       c.*1560

          .         .         .         .         .         .       g.25254
 ctctgtgctccatcctaggcaacagagtgatacgctgtttaaaaaggaaaaaatccttcc       c.*1620

          .         .         .         .         .         .       g.25314
 ctagagctagtatcctaaagctgcagagctagcccagacctcattggtttccttgtcctt       c.*1680

          .         .         .         .         .         .       g.25374
 ggggtgcttttcctgaatctttgcgggtgaagggagtgttgctcccagtccagaggcctg       c.*1740

          .         .         .         .         .         .       g.25434
 attctgtttggactgggttctcaagacacgaccaggttctcaagacacgagtccccttgt       c.*1800

          .         .         .         .         .         .       g.25494
 tcctccccattaaagggggtttgtcagaagcaagaacagcccctctccccagtcacagcc       c.*1860

          .         .         .         .         .         .       g.25554
 tgaagggaggccccgagagcttcctccttccccccacctgctccttaccttctctgccct       c.*1920

          .         .         .         .         .         .       g.25614
 gctttttagaactgcagttcattgttttaagggattgggggagggagcctggggacacaa       c.*1980

          .         .         .         .         .         .       g.25674
 accttttatacaatacaaagctttgctttttttttttttttcttccttttccctttctcg       c.*2040

          .         .         .         .         .         .       g.25734
 gttctcttctctcctctgaatggctgaagacccctctgccgagggaggttggggattgtg       c.*2100

          .         .         .         .         .         .       g.25794
 ggacaaggtcccttggtgctgatggcctgaaggggcctgagctgtgggcagatgcagttt       c.*2160

          .         .         .         .         .         .       g.25854
 tctgtgggcttggggaacctctcacgttgctgtgtcctggtgagcagcccgaccaataaa       c.*2220

          .                                                         g.25872
 cctgcttttctaaaagga                                                 c.*2238

 (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 Polymerase I and Transcript Release Factor (cavin-1) 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 mutations, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.