apolipoprotein E (APOE) - coding DNA reference sequence

(used for variant description)

(last modified August 11, 2013)

This file was created to facilitate the description of sequence variants on transcript NM_000041.2 in the APOE gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_007084.2, covering APOE transcript NM_000041.2.

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

 (upstream sequence)
                                         .         .                g.5023
                                      gggatccttgagtcctactcagc       c.-61

 .         .         .         .       | 02 .         .             g.5843
 cccagcggaggtgaaggacgtccttccccaggagccg | actggccaatcacaggcaggaag    c.-1

          .         .         .         .    | 03    .         .    g.6995
 ATGAAGGTTCTGTGGGCTGCGTTGCTGGTCACATTCCTGGCAG | GATGCCAGGCCAAGGTG    c.60
 M  K  V  L  W  A  A  L  L  V  T  F  L  A  G |   C  Q  A  K  V      p.20

          .         .         .         .         .         .       g.7055
 GAGCAAGCGGTGGAGACAGAGCCGGAGCCCGAGCTGCGCCAGCAGACCGAGTGGCAGAGC       c.120
 E  Q  A  V  E  T  E  P  E  P  E  L  R  Q  Q  T  E  W  Q  S         p.40

          .         .         .         .         .         .       g.7115
 GGCCAGCGCTGGGAACTGGCACTGGGTCGCTTTTGGGATTACCTGCGCTGGGTGCAGACA       c.180
 G  Q  R  W  E  L  A  L  G  R  F  W  D  Y  L  R  W  V  Q  T         p.60

          .         .         .         .         .       | 04 .    g.7755
 CTGTCTGAGCAGGTGCAGGAGGAGCTGCTCAGCTCCCAGGTCACCCAGGAACTGAG | GGCG    c.240
 L  S  E  Q  V  Q  E  E  L  L  S  S  Q  V  T  Q  E  L  R  |  A      p.80

          .         .         .         .         .         .       g.7815
 CTGATGGACGAGACCATGAAGGAGTTGAAGGCCTACAAATCGGAACTGGAGGAACAACTG       c.300
 L  M  D  E  T  M  K  E  L  K  A  Y  K  S  E  L  E  E  Q  L         p.100

          .         .         .         .         .         .       g.7875
 ACCCCGGTGGCGGAGGAGACGCGGGCACGGCTGTCCAAGGAGCTGCAGGCGGCGCAGGCC       c.360
 T  P  V  A  E  E  T  R  A  R  L  S  K  E  L  Q  A  A  Q  A         p.120

          .         .         .         .         .         .       g.7935
 CGGCTGGGCGCGGACATGGAGGACGTGTGCGGCCGCCTGGTGCAGTACCGCGGCGAGGTG       c.420
 R  L  G  A  D  M  E  D  V  C  G  R  L  V  Q  Y  R  G  E  V         p.140

          .         .         .         .         .         .       g.7995
 CAGGCCATGCTCGGCCAGAGCACCGAGGAGCTGCGGGTGCGCCTCGCCTCCCACCTGCGC       c.480
 Q  A  M  L  G  Q  S  T  E  E  L  R  V  R  L  A  S  H  L  R         p.160

          .         .         .         .         .         .       g.8055
 AAGCTGCGTAAGCGGCTCCTCCGCGATGCCGATGACCTGCAGAAGCGCCTGGCAGTGTAC       c.540
 K  L  R  K  R  L  L  R  D  A  D  D  L  Q  K  R  L  A  V  Y         p.180

          .         .         .         .         .         .       g.8115
 CAGGCCGGGGCCCGCGAGGGCGCCGAGCGCGGCCTCAGCGCCATCCGCGAGCGCCTGGGG       c.600
 Q  A  G  A  R  E  G  A  E  R  G  L  S  A  I  R  E  R  L  G         p.200

          .         .         .         .         .         .       g.8175
 CCCCTGGTGGAACAGGGCCGCGTGCGGGCCGCCACTGTGGGCTCCCTGGCCGGCCAGCCG       c.660
 P  L  V  E  Q  G  R  V  R  A  A  T  V  G  S  L  A  G  Q  P         p.220

          .         .         .         .         .         .       g.8235
 CTACAGGAGCGGGCCCAGGCCTGGGGCGAGCGGCTGCGCGCGCGGATGGAGGAGATGGGC       c.720
 L  Q  E  R  A  Q  A  W  G  E  R  L  R  A  R  M  E  E  M  G         p.240

          .         .         .         .         .         .       g.8295
 AGCCGGACCCGCGACCGCCTGGACGAGGTGAAGGAGCAGGTGGCGGAGGTGCGCGCCAAG       c.780
 S  R  T  R  D  R  L  D  E  V  K  E  Q  V  A  E  V  R  A  K         p.260

          .         .         .         .         .         .       g.8355
 CTGGAGGAGCAGGCCCAGCAGATACGCCTGCAGGCCGAGGCCTTCCAGGCCCGCCTCAAG       c.840
 L  E  E  Q  A  Q  Q  I  R  L  Q  A  E  A  F  Q  A  R  L  K         p.280

          .         .         .         .         .         .       g.8415
 AGCTGGTTCGAGCCCCTGGTGGAAGACATGCAGCGCCAGTGGGCCGGGCTGGTGGAGAAG       c.900
 S  W  F  E  P  L  V  E  D  M  Q  R  Q  W  A  G  L  V  E  K         p.300

          .         .         .         .         .                 g.8469
 GTGCAGGCTGCCGTGGGCACCAGCGCCGCCCCTGTGCCCAGCGACAATCACTGA             c.954
 V  Q  A  A  V  G  T  S  A  A  P  V  P  S  D  N  H  X               p.317

          .         .         .         .         .         .       g.8529
 acgccgaagcctgcagccatgcgaccccacgccaccccgtgcctcctgcctccgcgcagc       c.*60

          .         .         .         .         .         .       g.8589
 ctgcagcgggagaccctgtccccgccccagccgtcctcctggggtggaccctagtttaat       c.*120

          .         .                                               g.8612
 aaagattcaccaagtttcacgca                                            c.*143

 (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 Apolipoprotein E 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.