CD40 molecule, TNF receptor superfamily member 5 (CD40) - coding DNA reference sequence

(used for variant description)

(last modified July 27, 2015)

This file was created to facilitate the description of sequence variants on transcript NM_001250.4 in the CD40 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_007279.1, covering CD40 transcript NM_001250.4.

Please note that introns are available by clicking on the exon numbers above the sequence. 
 (upstream sequence)
                                                   .                g.5017
                                            gccaaggctggggcagg       c.-61

 .         .         .         .         .         .                g.5077
 ggagtcagcagaggcctcgctcgggcgcccagtggtcctgccgcctggtctcacctcgct       c.-1

          .         .         .         .         .  | 02      .    g.8562
 ATGGTTCGTCTGCCTCTGCAGTGCGTCCTCTGGGGCTGCTTGCTGACCGCT | GTCCATCCA    c.60
 M  V  R  L  P  L  Q  C  V  L  W  G  C  L  L  T  A   | V  H  P      p.20

          .         .         .         .         .         .       g.8622
 GAACCACCCACTGCATGCAGAGAAAAACAGTACCTAATAAACAGTCAGTGCTGTTCTTTG       c.120
 E  P  P  T  A  C  R  E  K  Q  Y  L  I  N  S  Q  C  C  S  L         p.40

          . | 03       .         .         .         .         .    g.9016
 TGCCAGCCAG | GACAGAAACTGGTGAGTGACTGCACAGAGTTCACTGAAACGGAATGCCTT    c.180
 C  Q  P  G |   Q  K  L  V  S  D  C  T  E  F  T  E  T  E  C  L      p.60

          .         .         .         .         .         .       g.9076
 CCTTGCGGTGAAAGCGAATTCCTAGACACCTGGAACAGAGAGACACACTGCCACCAGCAC       c.240
 P  C  G  E  S  E  F  L  D  T  W  N  R  E  T  H  C  H  Q  H         p.80

          .       | 04 .         .         .         .         .    g.9387
 AAATACTGCGACCCCA | ACCTAGGGCTTCGGGTCCAGCAGAAGGGCACCTCAGAAACAGAC    c.300
 K  Y  C  D  P  N |   L  G  L  R  V  Q  Q  K  G  T  S  E  T  D      p.100

          .         .         .         .         .         .       g.9447
 ACCATCTGCACCTGTGAAGAAGGCTGGCACTGTACGAGTGAGGCCTGTGAGAGCTGTGTC       c.360
 T  I  C  T  C  E  E  G  W  H  C  T  S  E  A  C  E  S  C  V         p.120

          .         .         .         .    | 05    .         .    g.9876
 CTGCACCGCTCATGCTCGCCCGGCTTTGGGGTCAAGCAGATTG | CTACAGGGGTTTCTGAT    c.420
 L  H  R  S  C  S  P  G  F  G  V  K  Q  I  A |   T  G  V  S  D      p.140

          .         .         .         .         .         .       g.9936
 ACCATCTGCGAGCCCTGCCCAGTCGGCTTCTTCTCCAATGTGTCATCTGCTTTCGAAAAA       c.480
 T  I  C  E  P  C  P  V  G  F  F  S  N  V  S  S  A  F  E  K         p.160

          .        | 06.         .         .         .         .    g.13416
 TGTCACCCTTGGACAAG | CTGTGAGACCAAAGACCTGGTTGTGCAACAGGCAGGCACAAAC    c.540
 C  H  P  W  T  S  |  C  E  T  K  D  L  V  V  Q  Q  A  G  T  N      p.180

          .          | 07        .         .         .         .    g.14912
 AAGACTGATGTTGTCTGTG | GTCCCCAGGATCGGCTGAGAGCCCTGGTGGTGATCCCCATC    c.600
 K  T  D  V  V  C  G |   P  Q  D  R  L  R  A  L  V  V  I  P  I      p.200

          .         .         .         .       | 08 .         .    g.15077
 ATCTTCGGGATCCTGTTTGCCATCCTCTTGGTGCTGGTCTTTATCA | AAAAGGTGGCCAAG    c.660
 I  F  G  I  L  F  A  I  L  L  V  L  V  F  I  K |   K  V  A  K      p.220

          .      | 09  .         .         .         .         .    g.15660
 AAGCCAACCAATAAG | GCCCCCCACCCCAAGCAGGAACCCCAGGAGATCAATTTTCCCGAC    c.720
 K  P  T  N  K   | A  P  H  P  K  Q  E  P  Q  E  I  N  F  P  D      p.240

          .         .         .         .         .         .       g.15720
 GATCTTCCTGGCTCCAACACTGCTGCTCCAGTGCAGGAGACTTTACATGGATGCCAACCG       c.780
 D  L  P  G  S  N  T  A  A  P  V  Q  E  T  L  H  G  C  Q  P         p.260

          .         .         .         .         .                 g.15774
 GTCACCCAGGAGGATGGCAAAGAGAGTCGCATCTCAGTGCAGGAGAGACAGTGA             c.834
 V  T  Q  E  D  G  K  E  S  R  I  S  V  Q  E  R  Q  X               p.277

          .         .         .         .         .         .       g.15834
 ggctgcacccacccaggagtgtggccacgtgggcaaacaggcagttggccagagagcctg       c.*60

          .         .         .         .         .         .       g.15894
 gtgctgctgctgctgtggcgtgagggtgaggggctggcactgactgggcatagctccccg       c.*120

          .         .         .         .         .         .       g.15954
 cttctgcctgcacccctgcagtttgagacaggagacctggcactggatgcagaaacagtt       c.*180

          .         .         .         .         .         .       g.16014
 caccttgaagaacctctcacttcaccctggagcccatccagtctcccaacttgtattaaa       c.*240

          .         .         .         .         .         .       g.16074
 gacagaggcagaagtttggtggtggtggtgttggggtatggtttagtaatatccaccaga       c.*300

          .         .         .         .         .         .       g.16134
 ccttccgatccagcagtttggtgcccagagaggcatcatggtggcttccctgcgcccagg       c.*360

          .         .         .         .         .         .       g.16194
 aagccatatacacagatgcccattgcagcattgtttgtgatagtgaacaactggaagctg       c.*420

          .         .         .         .         .         .       g.16254
 cttaactgtccatcagcaggagactggctaaataaaattagaatatatttatacaacaga       c.*480

          .         .         .         .         .         .       g.16314
 atctcaaaaacactgttgagtaaggaaaaaaaggcatgctgctgaatgatgggtatggaa       c.*540

          .         .         .         .         .         .       g.16374
 ctttttaaaaaagtacatgcttttatgtatgtatattgcctatggatatatgtataaata       c.*600

          .         .         .         .         .         .       g.16434
 caatatgcatcatatattgatataacaagggttctggaagggtacacagaaaacccacag       c.*660

          .         .         .         .                           g.16479
 ctcgaagagtggtgacgtctggggtggggaagaagggtctggggg                      c.*705

 (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 10th nucleotide is indicated by a "." above the sequence. The CD40 molecule, TNF receptor superfamily member 5 protein sequence is shown below the coding DNA sequence, with numbering indicated at the right starting with 1 for the translation initiating Methionine. Every 10th 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.

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