Bridging INtegrator 1 (BIN1) - coding DNA reference sequence

(used for mutation description)

(last modified March 12, 2010)


This file was created to facilitate the description of sequence variants in the BIN1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_012042.1, covering BIN1 transcript NM_139343.1 but including exon 11. Transcription of the BIN1 gene generates a range of differentially spliced products, with or without exons 7, 11, 13, 14, 15, 16 and 17.

NOTE: compared to the paper of Nicot et al. (2007), this reference sequence includes exon 11.

Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                     .         .         .         .                g.5045
                cgcgcccctccctcctcgcggacctggcggtgccggcgcccggag       c.-301

 .         .         .         .         .         .                g.5105
 tggccctttaaaaggcagcttattgtccggagggggcgggcggggggcgccgaccgcggc       c.-241

 .         .         .         .         .         .                g.5165
 ctgaggcccggcccctcccctctccctccctctgtccccgcgtcgctcgctggctagctc       c.-181

 .         .         .         .         .         .                g.5225
 gctggctcgctcgcccgtccggcgcacgctccgcctccgtcagttggctccgctgtcggg       c.-121

 .         .         .         .         .         .                g.5285
 tgcgcggcgtggagcggcagccggtctggacgcgcggccggggctgggggctgggagcgc       c.-61

 .         .         .         .         .         .                g.5345
 ggcgcgcaagatctccccgcgcgagagcggcccctgccaccgggcgaggcctgcgccgcg       c.-1

          .         .         .         .         .         .       g.5405
 ATGGCAGAGATGGGCAGTAAAGGGGTGACGGCGGGAAAGATCGCCAGCAACGTGCAGAAG       c.60
 M  A  E  M  G  S  K  G  V  T  A  G  K  I  A  S  N  V  Q  K         p.20

          .         .     | 02   .         .         .         .    g.35618
 AAGCTCACCCGCGCGCAGGAGAAG | GTTCTCCAGAAGCTGGGGAAGGCAGATGAGACCAAG    c.120
 K  L  T  R  A  Q  E  K   | V  L  Q  K  L  G  K  A  D  E  T  K      p.40

          .         .         .         .      | 03  .         .    g.41487
 GATGAGCAGTTTGAGCAGTGCGTCCAGAATTTCAACAAGCAGCTG | ACGGAGGGCACCCGG    c.180
 D  E  Q  F  E  Q  C  V  Q  N  F  N  K  Q  L   | T  E  G  T  R      p.60

          .         .         .         . | 04       .         .    g.41661
 CTGCAGAAGGATCTCCGGACCTACCTGGCCTCCGTCAAAG | CCATGCACGAGGCTTCCAAG    c.240
 L  Q  K  D  L  R  T  Y  L  A  S  V  K  A |   M  H  E  A  S  K      p.80

          .         .         .         .         .         .       g.41721
 AAGCTGAATGAGTGTCTGCAGGAGGTGTATGAGCCCGATTGGCCCGGCAGGGATGAGGCA       c.300
 K  L  N  E  C  L  Q  E  V  Y  E  P  D  W  P  G  R  D  E  A         p.100

          .      | 05  .         .         .         .         .    g.42243
 AACAAGATCGCAGAG | AACAACGACCTGCTGTGGATGGATTACCACCAGAAGCTGGTGGAC    c.360
 N  K  I  A  E   | N  N  D  L  L  W  M  D  Y  H  Q  K  L  V  D      p.120

          .         .         .         .         .  | 06      .    g.43266
 CAGGCGCTGCTGACCATGGACACGTACCTGGGCCAGTTCCCCGACATCAAG | TCACGCATT    c.420
 Q  A  L  L  T  M  D  T  Y  L  G  Q  F  P  D  I  K   | S  R  I      p.140

          .         .         .         .         .         .       g.43326
 GCCAAGCGGGGGCGCAAGCTGGTGGACTACGACAGTGCCCGGCACCACTACGAGTCCCTT       c.480
 A  K  R  G  R  K  L  V  D  Y  D  S  A  R  H  H  Y  E  S  L         p.160

          .         .         .          | 07        .         .    g.44054
 CAAACTGCCAAAAAGAAGGATGAAGCCAAAATTGCCAAG | CCTGTCTCGCTGCTTGAGAAA    c.540
 Q  T  A  K  K  K  D  E  A  K  I  A  K   | P  V  S  L  L  E  K      p.180
                                         ^  alternatively spliced exon

          .         .         .         .         .         .       g.44114
 GCCGCCCCCCAGTGGTGCCAAGGCAAACTGCAGGCTCATCTCGTAGCTCAAACTAACCTG       c.600
 A  A  P  Q  W  C  Q  G  K  L  Q  A  H  L  V  A  Q  T  N  L         p.200

          .   | 08     .         .         .         .         .    g.48318
 CTCCGAAATCAG | GCCGAGGAGGAGCTCATCAAAGCCCAGAAGGTGTTTGAGGAGATGAAT    c.660
 L  R  N  Q   | A  E  E  E  L  I  K  A  Q  K  V  F  E  E  M  N      p.220

          .         .         .         | 09         .         .    g.48664
 GTGGATCTGCAGGAGGAGCTGCCGTCCCTGTGGAACAG | CCGCGTAGGTTTCTACGTCAAC    c.720
 V  D  L  Q  E  E  L  P  S  L  W  N  S  |  R  V  G  F  Y  V  N      p.240

          .         .         .         .         .     | 10   .    g.50097
 ACGTTCCAGAGCATCGCGGGCCTGGAGGAAAACTTCCACAAGGAGATGAGCAAG | CTCAAC    c.780
 T  F  Q  S  I  A  G  L  E  E  N  F  H  K  E  M  S  K   | L  N      p.260

          .         .         .         .         .         .       g.50157
 CAGAACCTCAATGATGTGCTGGTCGGCCTGGAGAAGCAACACGGGAGCAACACCTTCACG       c.840
 Q  N  L  N  D  V  L  V  G  L  E  K  Q  H  G  S  N  T  F  T         p.280

          .        | 11.         .         .         .         .    g.51691
 GTCAAGGCCCAGCCCAG | AAAGAAAAGTAAACTGTTTTCGCGGCTGCGCAGAAAGAAGAAC    c.900
 V  K  A  Q  P  R  |  K  K  S  K  L  F  S  R  L  R  R  K  K  N      p.300
                   ^  alternatively spliced exon

    | 12     .         .         .         .         .         .    g.53191
 AG | TGACAACGCGCCTGCAAAAGGGAACAAGAGCCCTTCGCCTCCAGATGGCTCCCCTGCC    c.960
 S  |  D  N  A  P  A  K  G  N  K  S  P  S  P  P  D  G  S  P  A      p.320

          .         .         .         .         .         .       g.53251
 GCCACCCCCGAGATCAGAGTCAACCACGAGCCAGAGCCGGCCGGCGGGGCCACGCCCGGG       c.1020
 A  T  P  E  I  R  V  N  H  E  P  E  P  A  G  G  A  T  P  G         p.340

          .         .        | 13.         .         .         .    g.54720
 GCCACCCTCCCCAAGTCCCCATCTCAG | CTCCGGAAAGGCCCACCAGTCCCTCCGCCTCCC    c.1080
 A  T  L  P  K  S  P  S  Q   | L  R  K  G  P  P  V  P  P  P  P      p.360
                             ^  alternatively spliced exon

          .         .         .         .         .         .       g.54780
 AAACACACCCCGTCCAAGGAAGTCAAGCAGGAGCAGATCCTCAGCCTGTTTGAGGACACG       c.1140
 K  H  T  P  S  K  E  V  K  Q  E  Q  I  L  S  L  F  E  D  T         p.380

          .         .         .       | 14 .         .         .    g.58300
 TTTGTCCCTGAGATCAGCGTGACCACCCCCTCCCAG | TTTGAGGCCCCGGGGCCTTTCTCG    c.1200
 F  V  P  E  I  S  V  T  T  P  S  Q   | F  E  A  P  G  P  F  S      p.400
                                      ^  alternatively spliced exon

          .         .         .         .         .         .       g.58360
 GAGCAGGCCAGTCTGCTGGACCTGGACTTTGACCCCCTCCCGCCCGTGACGAGCCCTGTG       c.1260
 E  Q  A  S  L  L  D  L  D  F  D  P  L  P  P  V  T  S  P  V         p.420

          .         .     | 15   .         .         | 16         . g.59938
 AAGGCACCCACGCCCTCTGGTCAG | TCAATTCCATGGGACCTCTGGGAG | CCCACAGAGAGT c.1320
 K  A  P  T  P  S  G  Q   | S  I  P  W  D  L  W  E   | P  T  E  S   p.440
                          ^                          ^  alternatively spliced exons

          .         .         .         .         .         .       g.59998
 CCAGCCGGCAGCCTGCCTTCCGGGGAGCCCAGCGCTGCCGAGGGCACCTTTGCTGTGTCC       c.1380
 P  A  G  S  L  P  S  G  E  P  S  A  A  E  G  T  F  A  V  S         p.460

          .         .         .       | 17 .         .         .    g.61069
 TGGCCCAGCCAGACGGCCGAGCCGGGGCCTGCCCAA | CCAGCAGAGGCCTCGGAGGTGGCG    c.1440
 W  P  S  Q  T  A  E  P  G  P  A  Q   | P  A  E  A  S  E  V  A      p.480
                                       ^  alternatively spliced exon

          .         .         .         .         .         .       g.61129
 GGTGGGACCCAACCTGCGGCTGGAGCCCAGGAGCCAGGGGAGACGGCGGCAAGTGAAGCA       c.1500
 G  G  T  Q  P  A  A  G  A  Q  E  P  G  E  T  A  A  S  E  A         p.500

        | 18 .         .         .         .         .         .    g.61430
 GCCTCC | AGCTCTCTTCCTGCTGTCGTGGTGGAGACCTTCCCAGCAACTGTGAATGGCACC    c.1560
 A  S   | S  S  L  P  A  V  V  V  E  T  F  P  A  T  V  N  G  T      p.520

          .         .         .         .         .        | 19.    g.61769
 GTGGAGGGCGGCAGTGGGGCCGGGCGCTTGGACCTGCCCCCAGGTTTCATGTTCAAG | GTA    c.1620
 V  E  G  G  S  G  A  G  R  L  D  L  P  P  G  F  M  F  K   | V      p.540

          .         .         .         .         .         .       g.61829
 CAGGCCCAGCACGACTACACGGCCACTGACACAGACGAGCTGCAGCTCAAGGCTGGTGAT       c.1680
 Q  A  Q  H  D  Y  T  A  T  D  T  D  E  L  Q  L  K  A  G  D         p.560

          .         .         .          | 20        .         .    g.63676
 GTGGTGCTGGTGATCCCCTTCCAGAACCCTGAAGAGCAG | GATGAAGGCTGGCTCATGGGC    c.1740
 V  V  L  V  I  P  F  Q  N  P  E  E  Q   | D  E  G  W  L  M  G      p.580

          .         .         .         .         .         .       g.63736
 GTGAAGGAGAGCGACTGGAACCAGCACAAGGAGCTGGAGAAGTGCCGTGGCGTCTTCCCC       c.1800
 V  K  E  S  D  W  N  Q  H  K  E  L  E  K  C  R  G  V  F  P         p.600

          .         .                                               g.63763
 GAGAACTTCACTGAGAGGGTCCCATGA                                        c.1827
 E  N  F  T  E  R  V  P  X                                          p.608

          .         .         .         .         .         .       g.63823
 cggcggggcccaggcagcctccgggcgtgtgaagaacacctcctcccgaaaaatgtgtgg       c.*60

          .         .         .         .         .         .       g.63883
 ttcttttttttgttttgttttcgtttttcatcttttgaagagcaaagggaaatcaagagg       c.*120

          .         .         .         .         .         .       g.63943
 agacccccaggcagaggggcgttctcccaaagattaggtcgttttccaaagagccgcgtc       c.*180

          .         .         .         .         .         .       g.64003
 ccggcaagtccggcggaattcaccagtgttcctgaagctgctgtgtcctctagttgagtt       c.*240

          .         .         .         .         .         .       g.64063
 tctggcgcccctgcctgtgcccgcatgtgtgcctggccgcagggcggggctgggggctgc       c.*300

          .         .         .         .         .         .       g.64123
 cgagccaccatgcttgcctgaagcttcggccgcgccacccgggcaagggtcctcttttcc       c.*360

          .         .         .         .         .         .       g.64183
 tggcagctgctgtgggtggggcccagacaccagcctagcctggctctgccccgcagacgg       c.*420

          .         .         .         .         .         .       g.64243
 tctgtgtgctgtttgaaaataaatcttagtgttcaaaacaaaatgaaacaaaaaaaaaat       c.*480

          .                                                         g.64257
 gataaaaactctca                                                     c.*494

 (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 Bridging INtegrator 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 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 mutations, 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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