junctional adhesion molecule 3 (JAM3) - coding DNA reference sequence

(used for variant description)

(last modified August 22, 2012)

This file was created to facilitate the description of sequence variants on transcript NM_032801.4 in the JAM3 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NC_000011.9, covering JAM3 transcript NM_032801.4.

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

 (upstream sequence)
                               .         .         .                g.5039
                      tagacctcagcttcctctgtcaccatggtgccggctcgg       c.-121

 .         .         .         .         .         .                g.5099
 ctgggcccggcggtcgccatggtaactggggcgggtcgcagggtcctggcaggctgggcg       c.-61

 .         .         .         .         .         .                g.5159
 catgcgcgcggggactacaagccgcgccgcgctgccgctggcccctcagcaaccctcgac       c.-1

          .         .         .         .         .         .       g.5219
 ATGGCGCTGAGGCGGCCACCGCGACTCCGGCTCTGCGCTCGGCTGCCTGACTTCTTCCTG       c.60
 M  A  L  R  R  P  P  R  L  R  L  C  A  R  L  P  D  F  F  L         p.20

          .       | 02 .         .         .         .         .    g.75970
 CTGCTGCTTTTCAGGG | GCTGCCTGATAGGGGCTGTAAATCTCAAATCCAGCAATCGAACC    c.120
 L  L  L  F  R  G |   C  L  I  G  A  V  N  L  K  S  S  N  R  T      p.40

          .         .   | 03     .         .         .         .    g.76770
 CCAGTGGTACAGGAATTTGAAA | GTGTGGAACTGTCTTGCATCATTACGGATTCGCAGACA    c.180
 P  V  V  Q  E  F  E  S |   V  E  L  S  C  I  I  T  D  S  Q  T      p.60

          .         .         .         .         .         .       g.76830
 AGTGACCCCAGGATCGAGTGGAAGAAAATTCAAGATGAACAAACCACATATGTGTTTTTT       c.240
 S  D  P  R  I  E  W  K  K  I  Q  D  E  Q  T  T  Y  V  F  F         p.80

          .       | 04 .         .         .         .         .    g.80360
 GACAACAAAATTCAGG | GAGACTTGGCGGGTCGTGCAGAAATACTGGGGAAGACATCCCTG    c.300
 D  N  K  I  Q  G |   D  L  A  G  R  A  E  I  L  G  K  T  S  L      p.100

          .         .         .         .         .         .       g.80420
 AAGATCTGGAATGTGACACGGAGAGACTCAGCCCTTTATCGCTGTGAGGTCGTTGCTCGA       c.360
 K  I  W  N  V  T  R  R  D  S  A  L  Y  R  C  E  V  V  A  R         p.120

          .         .         .         .          | 05        .    g.80878
 AATGACCGCAAGGAAATTGATGAGATTGTGATCGAGTTAACTGTGCAAG | TGAAGCCAGTG    c.420
 N  D  R  K  E  I  D  E  I  V  I  E  L  T  V  Q  V |   K  P  V      p.140

          .         .         .         .         .         .       g.80938
 ACCCCTGTCTGTAGAGTGCCGAAGGCTGTACCAGTAGGCAAGATGGCAACACTGCACTGC       c.480
 T  P  V  C  R  V  P  K  A  V  P  V  G  K  M  A  T  L  H  C         p.160

          .         .         .         .         .         .       g.80998
 CAGGAGAGTGAGGGCCACCCCCGGCCTCACTACAGCTGGTATCGCAATGATGTACCACTG       c.540
 Q  E  S  E  G  H  P  R  P  H  Y  S  W  Y  R  N  D  V  P  L         p.180

          .         .         .         .         .         .       g.81058
 CCCACGGATTCCAGAGCCAATCCCAGATTTCGCAATTCTTCTTTCCACTTAAACTCTGAA       c.600
 P  T  D  S  R  A  N  P  R  F  R  N  S  S  F  H  L  N  S  E         p.200

          .   | 06     .         .         .         .         .    g.82069
 ACAGGCACTTTG | GTGTTCACTGCTGTTCACAAGGACGACTCTGGGCAGTACTACTGCATT    c.660
 T  G  T  L   | V  F  T  A  V  H  K  D  D  S  G  Q  Y  Y  C  I      p.220

          .         .         .         .         .   | 07     .    g.84630
 GCTTCCAATGACGCAGGCTCAGCCAGGTGTGAGGAGCAGGAGATGGAAGTCT | ATGACCTG    c.720
 A  S  N  D  A  G  S  A  R  C  E  E  Q  E  M  E  V  Y |   D  L      p.240

          .         .         .         .         .         .       g.84690
 AACATTGGCGGAATTATTGGGGGGGTTCTGGTTGTCCTTGCTGTACTGGCCCTGATCACG       c.780
 N  I  G  G  I  I  G  G  V  L  V  V  L  A  V  L  A  L  I  T         p.260

          .         .         .         .         .         .       g.84750
 TTGGGCATCTGCTGTGCATACAGACGTGGCTACTTCATCAACAATAAACAGGATGGAGAA       c.840
 L  G  I  C  C  A  Y  R  R  G  Y  F  I  N  N  K  Q  D  G  E         p.280

    | 08     .         .         .         .         .        | 09. g.85224
 AG | TTACAAGAACCCAGGGAAACCAGATGGAGTTAACTACATCCGCACTGACGAGGAG | GGC c.900
 S  |  Y  K  N  P  G  K  P  D  G  V  N  Y  I  R  T  D  E  E   | G   p.300

          .         .         .                                     g.85257
 GACTTCAGACACAAGTCATCGTTTGTGATCTGA                                  c.933
 D  F  R  H  K  S  S  F  V  I  X                                    p.310

          .         .         .         .         .         .       g.85317
 gacccgcggtgtggctgagagcgcacagagcgcacgtgcacatacctctgctagaaactc       c.*60

          .         .         .         .         .         .       g.85377
 ctgtcaaggcagcgagagctgatgcactcggacagagctagacactcattcagaagcttt       c.*120

          .         .         .         .         .         .       g.85437
 tcgttttggccaaagttgaccactactcttcttactctaacaagccacatgaatagaaga       c.*180

          .         .         .         .         .         .       g.85497
 attttcctcaagatggacccggtaaatataaccacaaggaagcgaaactgggtgcgttca       c.*240

          .         .         .         .         .         .       g.85557
 ctgagttgggttcctaatctgtttctggcctgattcccgcatgagtattagggtgatctt       c.*300

          .         .         .         .         .         .       g.85617
 aaagagtttgctcacgtaaacgcccgtgctgggccctgtgaagccagcatgttcaccact       c.*360

          .         .         .         .         .         .       g.85677
 ggtcgttcagcagccacgacagcaccatgtgagatggcgaggtggctggacagcaccagc       c.*420

          .         .         .         .         .         .       g.85737
 agcgcatcccggcgggaacccagaaaaggcttcttacacagcagccttacttcatcggcc       c.*480

          .         .         .         .         .         .       g.85797
 cacagacaccaccgcagtttcttcttaaaggctctgctgatcggtgttgcagtgtccatt       c.*540

          .         .         .         .         .         .       g.85857
 gtggagaagctttttggatcagcattttgtaaaaacaaccaaaatcaggaaggtaaattg       c.*600

          .         .         .         .         .         .       g.85917
 gttgctggaagagggatcttgcctgaggaaccctgcttgtccaacagggtgtcaggattt       c.*660

          .         .         .         .         .         .       g.85977
 aaggaaaaccttcgtcttaggctaagtctgaaatggtactgaaatatgcttttctatggg       c.*720

          .         .         .         .         .         .       g.86037
 tcttgtttattttataaaattttacatctaaatttttgctaaggatgtattttgattatt       c.*780

          .         .         .         .         .         .       g.86097
 gaaaagaaaatttctatttaaactgtaaatatattgtcatacaatgttaaataacctatt       c.*840

          .         .         .         .         .         .       g.86157
 tttttaaaaaagttcaacttaaggtagaagttccaagctactagtgttaaattggaaaat       c.*900

          .         .         .         .         .         .       g.86217
 atcaataattaagagtattttacccaaggaatcctctcatggaagtttactgtgatgttc       c.*960

          .         .         .         .         .         .       g.86277
 cttttctcacacaagttttagcctttttcacaagggaactcatactgtctacacatcaga       c.*1020

          .         .         .         .         .         .       g.86337
 ccatagttgcttaggaaacctttaaaaattccagttaagcaatgttgaaatcagtttgca       c.*1080

          .         .         .         .         .         .       g.86397
 tctcttcaaaagaaacctctcaggttagctttgaactgcctcttcctgagatgactagga       c.*1140

          .         .         .         .         .         .       g.86457
 cagtctgtacccagaggccacccagaagccctcagatgtacatacacagatgccagtcag       c.*1200

          .         .         .         .         .         .       g.86517
 ctcctggggttgcgccaggcgcccccgctctagctcactgttgcctcgctgtctgccagg       c.*1260

          .         .         .         .         .         .       g.86577
 aggccctgccatccttgggccctggcagtggctgtgtcccagtgagctttactcacgtgg       c.*1320

          .         .         .         .         .         .       g.86637
 cccttgcttcatccagcacagctctcaggtgggcactgcagggacactggtgtcttccat       c.*1380

          .         .         .         .         .         .       g.86697
 gtagcgtcccagctttgggctcctgtaacagacctctttttggttatggatggctcacaa       c.*1440

          .         .         .         .         .         .       g.86757
 aatagggcccccaatgctattttttttttttaagtttgtttaattatttgttaagattgt       c.*1500

          .         .         .         .         .         .       g.86817
 ctaaggccaaaggcaattgcgaaatcaagtctgtcaagtacaataacatttttaaaagaa       c.*1560

          .         .         .         .         .         .       g.86877
 aatggatcccactgttcctctttgccacagagaaagcacccagacgccacaggctctgtc       c.*1620

          .         .         .         .         .         .       g.86937
 gcatttcaaaacaaaccatgatggagtggcggccagtccagccttttaaagaacgtcagg       c.*1680

          .         .         .         .         .         .       g.86997
 tggagcagccaggtgaaaggcctggcggggaggaaagtgaaacgcctgaatcaaaagcag       c.*1740

          .         .         .         .         .         .       g.87057
 ttttctaattttgactttaaatttttcatccgccggagacactgctcccatttgtggggg       c.*1800

          .         .         .         .         .         .       g.87117
 gacattagcaacatcactcagaagcctgtgttcttcaagagcaggtgttctcagcctcac       c.*1860

          .         .         .         .         .         .       g.87177
 atgccctgccgtgctggactcaggactgaagtgctgtaaagcaaggagctgctgagaagg       c.*1920

          .         .         .         .         .         .       g.87237
 agcactccactgtgtgcctggagaatggctctcactactcaccttgtctttcagcttcca       c.*1980

          .         .         .         .         .         .       g.87297
 gtgtcttgggttttttatactttgacagcttttttttaattgcatacatgagactgtgtt       c.*2040

          .         .         .         .         .         .       g.87357
 gactttttttagttatgtgaaacactttgccgcaggccgcctggcagaggcaggaaatgc       c.*2100

          .         .         .         .         .         .       g.87417
 tccagcagtggctcagtgctccctggtgtctgctgcatggcatcctggatgcttagcatg       c.*2160

          .         .         .         .         .         .       g.87477
 caagttccctccatcattgccaccttggtagagagggatggctccccaccctcagcgttg       c.*2220

          .         .         .         .         .         .       g.87537
 gggattcacgctccagcctccttcttggttgtcatagtgatagggtagccttattgcccc       c.*2280

          .         .         .         .         .         .       g.87597
 ctcttcttataccctaaaaccttctacactagtgccatgggaaccaggtctgaaaaagta       c.*2340

          .         .         .         .         .         .       g.87657
 gagagaagtgaaagtagagtctgggaagtagctgcctataactgagactagacggaaaag       c.*2400

          .         .         .         .         .         .       g.87717
 gaatactcgtgtattttaagatatgaatgtgactcaagactcgaggccgatacgaggctg       c.*2460

          .         .         .         .         .         .       g.87777
 tgattctgcctttggatggatgttgctgtacacagatgctacagacttgtactaacacac       c.*2520

          .         .         .         .         .                 g.87833
 cgtaatttggcatttgtttaacctcatttataaaagcttcaaaaaaacccaaacat           c.*2576

 (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 Junctional adhesion molecule 3 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.