family with sequence similarity 109, member A (FAM109A) - coding DNA reference sequence

(used for variant description)

(last modified May 14, 2018)

This file was created to facilitate the description of sequence variants on transcript NM_001177996.1 in the FAM109A gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000012.11, covering FAM109A transcript NM_001177996.1.

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

 (upstream sequence)
                                         .         .                g.5020
                                         aggggcgcgcccgtgggtcg       c.-421

 .         .         .         .         .         .                g.5080
 cggactgtccggttgctcccgcctccttccgtcggatccgcgctctcccgcggctgcgcc       c.-361

 .         .         .         .         .         .                g.5140
 ggcccggccgcccaggagacaaagcgctgccgccgccgtcgccgccaccgggccagtccc       c.-301

 .         .         .         .         .         .                g.5200
 gaaccatggccgggccaccccgcaacctcgcgcctcccgtcccgtcgccgccctaggcct       c.-241

 .          | 02        .         .         .         .             g.7914
 gcgctgcgag | atgcagaaacagaggcccagagagatgaatagcctgcctggggtccccca    c.-181

 .         .         .         .         .         .                g.7974
 gcccagatgctgcagagctgacatttgaatccagagaagagcgagctgaggctggagctg       c.-121

 .         .         .         .     | 03   .         .             g.8495
 agcagagggcagggaggcaagtggtggcctgagag | tttgctgaggatgatggcttccagc    c.-61

 .         .         .         .         .         .                g.8555
 tccatctatttccccgcaaaggacatgatctcattcctttttatggctggatagttttcc       c.-1

     | 04    .         .         .         .         .         .    g.10715
 ATG | GCCCCAGGCTCCCCTCCAGGCCCCGCGATTGCCACCATGAAGCTGAACGAGCGCAGC    c.60
 M   | A  P  G  S  P  P  G  P  A  I  A  T  M  K  L  N  E  R  S      p.20

          .         .         .         .         .         .       g.10775
 CTGGCCTTCTACGCCACCTGTGACGCCCCGGTGGACAATGCAGGCTTCCTGTACAAGAAG       c.120
 L  A  F  Y  A  T  C  D  A  P  V  D  N  A  G  F  L  Y  K  K         p.40

          .         .         .         .         .         .       g.10835
 GGTGGGCGGCACGCGGCCTACCACCGGCGCTGGTTCGTGCTGCGCGGGAACATGCTCTTC       c.180
 G  G  R  H  A  A  Y  H  R  R  W  F  V  L  R  G  N  M  L  F         p.60

          .         .         .         .         .         .       g.10895
 TACTTCGAGGACGCTGCCAGCCGTGAGCCCGTGGGCGTCATCATCCTGGAGGGCTGCACT       c.240
 Y  F  E  D  A  A  S  R  E  P  V  G  V  I  I  L  E  G  C  T         p.80

          .         .         .         .         .         .       g.10955
 GTGGAGCTGGTGGAGGCCGCCGAGGAGTTCGCCTTCGCTGTGCGCTTTGCGGGGACCCGG       c.300
 V  E  L  V  E  A  A  E  E  F  A  F  A  V  R  F  A  G  T  R         p.100

          .         .         .         .         .         .       g.11015
 GCGCGCACCTACGTGCTGGCCGCTGAGAGTCAGGATGCCATGGAGGGCTGGGTCAAGGCC       c.360
 A  R  T  Y  V  L  A  A  E  S  Q  D  A  M  E  G  W  V  K  A         p.120

          .         .         .         .         .         .       g.11075
 CTGTCGCGTGCCAGCTTCGACTACCTGCGGCTGGTGGTGCGCGAGCTGGAGCAGCAGCTG       c.420
 L  S  R  A  S  F  D  Y  L  R  L  V  V  R  E  L  E  Q  Q  L         p.140

          .         .         .         .         .         .       g.11135
 GCGGCTGTACGTGGCGGGGGTGGCATGGCCCTGCCCCAGCCCCAGCCCCAGTCCCTGCCC       c.480
 A  A  V  R  G  G  G  G  M  A  L  P  Q  P  Q  P  Q  S  L  P         p.160

          .         .         .         .         .         .       g.11195
 TTGCCCCCGTCCCTGCCCTCTGCCCTGGCCCCAGTCCCATCCCTGCCTTCTGCCCCAGCC       c.540
 L  P  P  S  L  P  S  A  L  A  P  V  P  S  L  P  S  A  P  A         p.180

          .         .         .         .         .         .       g.11255
 CCGGTCCCAGCCCTGCCCCTGCCCCGCCGGCCCAGTGCCCTCCCGCCCAAGGAGAATGGC       c.600
 P  V  P  A  L  P  L  P  R  R  P  S  A  L  P  P  K  E  N  G         p.200

          .         .         .         .         .         .       g.11315
 TGCGCTGTCTGGAGCACTGAGGCCACCTTCAGGCCTGGACCCGAGCCCCCTCCACCACCG       c.660
 C  A  V  W  S  T  E  A  T  F  R  P  G  P  E  P  P  P  P  P         p.220

          .         .         .         .         .         .       g.11375
 CCTCGCCGCCGGGCCTCGGCACCCCACGGGCCCCTGGACATGGCCCCCTTCGCCCGGCTG       c.720
 P  R  R  R  A  S  A  P  H  G  P  L  D  M  A  P  F  A  R  L         p.240

          .         .         .         .         .         .       g.11435
 CACGAGTGCTATGGCCAGGAGATCCGGGCCCTGCGTGGCCAGTGGCTCAGCAGCCGGGTC       c.780
 H  E  C  Y  G  Q  E  I  R  A  L  R  G  Q  W  L  S  S  R  V         p.260

                                                                    g.11444
 CAGCCCTGA                                                          c.789
 Q  P  X                                                            p.262

          .         .         .         .         .         .       g.11504
 ggccaccagggcgcctgttttagggggacacaagctctatgccctctgggacaggccggg       c.*60

          .         .         .         .         .         .       g.11564
 tcctggagagactgggggagcagatcctgagggaaatcatgggcaaggctggcccccagg       c.*120

          .         .         .         .         .         .       g.11624
 ccctgagtggcctggttttgggggatgcaggctctgagaaggtgctggattctgagtggg       c.*180

          .         .         .         .         .         .       g.11684
 cctttaggaccatgtgacccagaaggcctacccttgaggggaacgtcacgtgcaacacta       c.*240

          .         .         .         .         .         .       g.11744
 aggagaatccagggcctgagggggaggtttcctgagaactccggccccaggctggcctga       c.*300

          .         .         .         .         .         .       g.11804
 gctgccgggcagaggcctgtgctggcaacaggcattgccgggcctgcagctcagagggtc       c.*360

          .         .         .         .         .         .       g.11864
 actgggactgagggcgatctgtggcctgaaaagcaaatgcacagttagtgcagctcctga       c.*420

          .         .         .         .         .         .       g.11924
 ccaggccttcagggtggacagagggaggatcggtcatggcagccacacctgggcctggcc       c.*480

          .         .         .         .         .         .       g.11984
 ttgctccgggacctgccagaggagctggcctggctctgtgcctgcctgcctccaggagca       c.*540

          .         .         .         .         .         .       g.12044
 ggacggtggctgggagggtagtgactggggacacaggtgcaggtgttagtgcaggaccgg       c.*600

          .         .         .         .         .         .       g.12104
 aagggtgaggtggcctggtcctcggggctcctggcctgggctggctgaggcaggactctg       c.*660

          .         .         .         .         .         .       g.12164
 ccaaaagtcccctgccaggcctcatggtggtgctcctggtggcagtggctctctggccgc       c.*720

          .         .         .         .         .         .       g.12224
 gggccctgtctgtgtctccgtggtggctctcacagggctctccagacactccttgactgc       c.*780

          .         .         .         .         .         .       g.12284
 atccttcagtcttggcccctaggcctggggccccttgggagcttgcctgacctcccttcc       c.*840

          .         .         .         .         .         .       g.12344
 tgggctgggtagccatggcccgaggtgaccttctagcaggttcccccagggaggggaggc       c.*900

          .         .         .         .         .         .       g.12404
 caccagctgactcaccgcctaggaaggcccaggtgctgacctagtggcggagaaaaagcc       c.*960

          .         .         .         .         .         .       g.12464
 gcacaccgagtgtggcttccagagcccctcttcagctccaggcagccccctctaacatgt       c.*1020

          .         .         .         .         .         .       g.12524
 cccctcctgagctcagcccccacccccatactcctggtggggaccaggtcttgcttggct       c.*1080

          .         .         .         .         .         .       g.12584
 tcggggctgaccgccggtcccctttcttctcaccacagtgcccatttttcatccagggag       c.*1140

          .         .         .         .         .         .       g.12644
 aacctcggggctgggacacctcctggccctcaccctgggtcatgtttacagtcctcagtg       c.*1200

          .         .         .         .         .         .       g.12704
 ccccacaccggtggccccctgaggacacctccaccctgaccttgattttcccaaacgctg       c.*1260

          .         .         .         .         .         .       g.12764
 cctcttggtgacagactcagcccaaaaccccttccttctgtctctggagacccttgagct       c.*1320

          .         .         .         .         .         .       g.12824
 tggggaaatatggaggggtgtgtgtctgcaatcaaggcctctgcagctcacggctggccc       c.*1380

          .         .         .         .         .         .       g.12884
 ggtgggctgggacttccgtctgaattttaaatacttagggttcatttttttttctctggc       c.*1440

          .         .         .         .         .         .       g.12944
 aacaaagcttgatgttttcactgctttagtttcctgtttgctggtgggaggggatacggt       c.*1500

          .         .         .         .         .         .       g.13004
 ctgtgactctggacttgctctgggggaacagttgtcactgcccccggggagaggggcagc       c.*1560

          .         .         .         .         .         .       g.13064
 ttgggctggagaagcacagccagagacagagcccctcgagagggatccttggctgcttca       c.*1620

          .         .         .         .         .         .       g.13124
 ttgtcttccccccagcaagccctgctctccacaggcacctctggggtcttggtatggtcc       c.*1680

          .         .         .         .         .         .       g.13184
 ccgctcacctccttccagagtcctgagtggtgtgggtgtgggtggcacaggatctggggc       c.*1740

          .         .         .         .         .         .       g.13244
 atgggaggggttcagagcttcccagagccccgtgtcctggcagactcagctggtgggctg       c.*1800

          .         .         .         .         .         .       g.13304
 gggtgttaaccccagtcctggcgtaggtttacagactctcaaggtacgttggccctggtc       c.*1860

          .         .         .         .         .         .       g.13364
 tcctgggagagaggggtgagggatgtcccctaccaaagcacaaggtgggatcaggctgcc       c.*1920

          .         .         .         .         .         .       g.13424
 tcctgggttgggtgtcgggggagctgtccggcagcctggcagggagatgcaagggctaaa       c.*1980

          .         .         .         .                           g.13471
 gtaaaattttgtcaagtaatggctgattgtgtcattttttttcccca                    c.*2027

 (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 Family with sequence similarity 109, member A 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.