sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A (SEMA4A) - coding DNA reference sequence

(used for mutation description)

(last modified February 29, 2012)


This file was created to facilitate the description of sequence variants in the SEMA4A gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_027683.1, covering SEMA4A transcript NM_001193301.1.


Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
           .         .         .         .         .                g.5059
  agagatgcggtcgccatggtgactgaggaccagtgaggcgggatggggttgagaatggg       c.-121

 .         .         .         .         .         .                g.5119
 ggtgggggtgtggcaggggctgaggcactgagagaccggaaagcctggcattccagaggg       c.-61

 .         .         .         . | 02       .         .             g.9635
 agggaaacgcagcggcatccccaggctccag | agctccctggtgacagtctgtggctgagc    c.-1

          .         .         .         .         .         .       g.9695
 ATGGCCCTCCCAGCCCTGGGCCTGGACCCCTGGAGCCTCCTGGGCCTTTTCCTCTTCCAA       c.60
 M  A  L  P  A  L  G  L  D  P  W  S  L  L  G  L  F  L  F  Q         p.20

          .         .         .         .         .         .       g.9755
 CTGCTTCAGCTGCTGCTGCCGACGACGACCGCGGGGGGAGGCGGGCAGGGGCCCATGCCC       c.120
 L  L  Q  L  L  L  P  T  T  T  A  G  G  G  G  Q  G  P  M  P         p.40

          .          | 03        .         .         .         .    g.11511
 AGGGTCAGATACTATGCAG | GGGATGAACGTAGGGCACTTAGCTTCTTCCACCAGAAGGGC    c.180
 R  V  R  Y  Y  A  G |   D  E  R  R  A  L  S  F  F  H  Q  K  G      p.60

          .         .         .         .         .         .       g.11571
 CTCCAGGATTTTGACACTCTGCTCCTGAGTGGTGATGGAAATACTCTCTACGTGGGGGCT       c.240
 L  Q  D  F  D  T  L  L  L  S  G  D  G  N  T  L  Y  V  G  A         p.80

          .         .         .         .         .         .       g.11631
 CGAGAAGCCATTCTGGCCTTGGATATCCAGGATCCAGGGGTCCCCAGGCTAAAGAACATG       c.300
 R  E  A  I  L  A  L  D  I  Q  D  P  G  V  P  R  L  K  N  M         p.100

  | 04       .         .         .         .         .         .    g.13186
  | ATACCGTGGCCAGCCAGTGACAGAAAAAAGAGTGAATGTGCCTTTAAGAAGAAGAGCAAT    c.360
  | I  P  W  P  A  S  D  R  K  K  S  E  C  A  F  K  K  K  S  N      p.120

     | 05    .         .         .         .         .         .    g.13501
 GAG | ACACAGTGTTTCAACTTCATCCGTGTCCTGGTTTCTTACAATGTCACCCATCTCTAC    c.420
 E   | T  Q  C  F  N  F  I  R  V  L  V  S  Y  N  V  T  H  L  Y      p.140

          .         .         .         .   | 06     .         .    g.13793
 ACCTGCGGCACCTTCGCCTTCAGCCCTGCTTGTACCTTCATT | GAACTTCAAGATTCCTAC    c.480
 T  C  G  T  F  A  F  S  P  A  C  T  F  I   | E  L  Q  D  S  Y      p.160

          .         .         .         .         .         .       g.13853
 CTGTTGCCCATCTCGGAGGACAAGGTCATGGAGGGAAAAGGCCAAAGCCCCTTTGACCCC       c.540
 L  L  P  I  S  E  D  K  V  M  E  G  K  G  Q  S  P  F  D  P         p.180

          .         .         | 07         .         .         .    g.15531
 GCTCACAAGCATACGGCTGTCTTGGTGG | ATGGGATGCTCTATTCTGGTACTATGAACAAC    c.600
 A  H  K  H  T  A  V  L  V  D |   G  M  L  Y  S  G  T  M  N  N      p.200

          .         .         .         .         .         .       g.15591
 TTCCTGGGCAGTGAGCCCATCCTGATGCGCACACTGGGATCCCAGCCTGTCCTCAAGACC       c.660
 F  L  G  S  E  P  I  L  M  R  T  L  G  S  Q  P  V  L  K  T         p.220

          .         .      | 08  .         .         .         .    g.15996
 GACAACTTCCTCCGCTGGCTGCATC | ATGACGCCTCCTTTGTGGCAGCCATCCCTTCGACC    c.720
 D  N  F  L  R  W  L  H  H |   D  A  S  F  V  A  A  I  P  S  T      p.240

          .         .         .         .         .         .       g.16056
 CAGGTCGTCTACTTCTTCTTCGAGGAGACAGCCAGCGAGTTTGACTTCTTTGAGAGGCTC       c.780
 Q  V  V  Y  F  F  F  E  E  T  A  S  E  F  D  F  F  E  R  L         p.260

          .         .         . | 09       .         .         .    g.16432
 CACACATCGCGGGTGGCTAGAGTCTGCAAG | AATGACGTGGGCGGCGAAAAGCTGCTGCAG    c.840
 H  T  S  R  V  A  R  V  C  K   | N  D  V  G  G  E  K  L  L  Q      p.280

          .         .         .         .         .         .       g.16492
 AAGAAGTGGACCACCTTCCTGAAGGCCCAGCTGCTCTGCACCCAGCCGGGGCAGCTGCCC       c.900
 K  K  W  T  T  F  L  K  A  Q  L  L  C  T  Q  P  G  Q  L  P         p.300

          .         .         .         .         .         .       g.16552
 TTCAACGTCATCCGCCACGCGGTCCTGCTCCCCGCCGATTCTCCCACAGCTCCCCACATC       c.960
 F  N  V  I  R  H  A  V  L  L  P  A  D  S  P  T  A  P  H  I         p.320

          .         .    | 10    .         .         .         .    g.18037
 TACGCAGTCTTCACCTCCCAGTG | GCAGGTTGGCGGGACCAGGAGCTCTGCGGTTTGTGCC    c.1020
 Y  A  V  F  T  S  Q  W  |  Q  V  G  G  T  R  S  S  A  V  C  A      p.340

          .         .         .         .         .         .       g.18097
 TTCTCTCTCTTGGACATTGAACGTGTCTTTAAGGGGAAATACAAAGAGTTGAACAAAGAA       c.1080
 F  S  L  L  D  I  E  R  V  F  K  G  K  Y  K  E  L  N  K  E         p.360

          .         .         .         .         .     | 11   .    g.27888
 ACTTCACGCTGGACTACTTATAGGGGCCCTGAGACCAACCCCCGGCCAGGCAGT | TGCTCA    c.1140
 T  S  R  W  T  T  Y  R  G  P  E  T  N  P  R  P  G  S   | C  S      p.380

          .         .         .         .         .         .       g.27948
 GTGGGCCCCTCCTCTGATAAGGCCCTGACCTTCATGAAGGACCATTTCCTGATGGATGAG       c.1200
 V  G  P  S  S  D  K  A  L  T  F  M  K  D  H  F  L  M  D  E         p.400

          .         .         .         .         .         .       g.28008
 CAAGTGGTGGGGACGCCCCTGCTGGTGAAATCTGGCGTGGAGTATACACGGCTTGCAGTG       c.1260
 Q  V  V  G  T  P  L  L  V  K  S  G  V  E  Y  T  R  L  A  V         p.420

          .         .         .         .         .      | 12  .    g.29883
 GAGACAGCCCAGGGCCTTGATGGGCACAGCCATCTTGTCATGTACCTGGGAACCA | CCACA    c.1320
 E  T  A  Q  G  L  D  G  H  S  H  L  V  M  Y  L  G  T  T |   T      p.440

          .         .         .         .         .         .       g.29943
 GGGTCGCTCCACAAGGCTGTGGTAAGTGGGGACAGCAGTGCTCATCTGGTGGAAGAGATT       c.1380
 G  S  L  H  K  A  V  V  S  G  D  S  S  A  H  L  V  E  E  I         p.460

          .         .         .         .         .     | 13   .    g.30148
 CAGCTGTTCCCTGACCCTGAACCTGTTCGCAACCTGCAGCTGGCCCCCACCCAG | GGTGCA    c.1440
 Q  L  F  P  D  P  E  P  V  R  N  L  Q  L  A  P  T  Q   | G  A      p.480

          .         .         .         .         .         .       g.30208
 GTGTTTGTAGGCTTCTCAGGAGGTGTCTGGAGGGTGCCCCGAGCCAACTGTAGTGTCTAT       c.1500
 V  F  V  G  F  S  G  G  V  W  R  V  P  R  A  N  C  S  V  Y         p.500

          .         .         .         .         .         .       g.30268
 GAGAGCTGTGTGGACTGTGTCCTTGCCCGGGACCCCCACTGTGCCTGGGACCCTGAGTCC       c.1560
 E  S  C  V  D  C  V  L  A  R  D  P  H  C  A  W  D  P  E  S         p.520

          .         .         .   | 14     .         .         .    g.30640
 CGAACCTGTTGCCTCCTGTCTGCCCCCAACCT | GAACTCCTGGAAGCAGGACATGGAGCGG    c.1620
 R  T  C  C  L  L  S  A  P  N  L  |  N  S  W  K  Q  D  M  E  R      p.540

          .         .         .         .         .         .       g.30700
 GGGAACCCAGAGTGGGCATGTGCCAGTGGCCCCATGAGCAGGAGCCTTCGGCCTCAGAGC       c.1680
 G  N  P  E  W  A  C  A  S  G  P  M  S  R  S  L  R  P  Q  S         p.560

          .    | 15    .         .         .         .         .    g.31508
 CGCCCGCAAATCA | TTAAAGAAGTCCTGGCTGTCCCCAACTCCATCCTGGAGCTCCCCTGC    c.1740
 R  P  Q  I  I |   K  E  V  L  A  V  P  N  S  I  L  E  L  P  C      p.580

          .         .         .         .         .         .       g.31568
 CCCCACCTGTCAGCCTTGGCCTCTTATTATTGGAGTCATGGCCCAGCAGCAGTCCCAGAA       c.1800
 P  H  L  S  A  L  A  S  Y  Y  W  S  H  G  P  A  A  V  P  E         p.600

          .         .         .         .         .         .       g.31628
 GCCTCTTCCACTGTCTACAATGGCTCCCTCTTGCTGATAGTGCAGGATGGAGTTGGGGGT       c.1860
 A  S  S  T  V  Y  N  G  S  L  L  L  I  V  Q  D  G  V  G  G         p.620

          .         .         .         .         .         .       g.31688
 CTCTACCAGTGCTGGGCAACTGAGAATGGCTTTTCATACCCTGTGATCTCCTACTGGGTG       c.1920
 L  Y  Q  C  W  A  T  E  N  G  F  S  Y  P  V  I  S  Y  W  V         p.640

          .         .         .         .         .         .       g.31748
 GACAGCCAGGACCAGACCCTGGCCCTGGATCCTGAACTGGCAGGCATCCCCCGGGAGCAT       c.1980
 D  S  Q  D  Q  T  L  A  L  D  P  E  L  A  G  I  P  R  E  H         p.660

          .         .         .         .         .         .       g.31808
 GTGAAGGTCCCGTTGACCAGGGTCAGTGGTGGGGCCGCCCTGGCTGCCCAGCAGTCCTAC       c.2040
 V  K  V  P  L  T  R  V  S  G  G  A  A  L  A  A  Q  Q  S  Y         p.680

          .         .         .         .         .         .       g.31868
 TGGCCCCACTTTGTCACTGTCACTGTCCTCTTTGCCTTAGTGCTTTCAGGAGCCCTCATC       c.2100
 W  P  H  F  V  T  V  T  V  L  F  A  L  V  L  S  G  A  L  I         p.700

          .         .         .         .         .         .       g.31928
 ATCCTCGTGGCCTCCCCATTGAGAGCACTCCGGGCTCGGGGCAAGGTTCAGGGCTGTGAG       c.2160
 I  L  V  A  S  P  L  R  A  L  R  A  R  G  K  V  Q  G  C  E         p.720

          .         .         .         .         .         .       g.31988
 ACCCTGCGCCCTGGGGAGAAGGCCCCGTTAAGCAGAGAGCAACACCTCCAGTCTCCCAAG       c.2220
 T  L  R  P  G  E  K  A  P  L  S  R  E  Q  H  L  Q  S  P  K         p.740

          .         .         .         .         .         .       g.32048
 GAATGCAGGACCTCTGCCAGTGATGTGGACGCTGACAACAACTGCCTAGGCACTGAGGTA       c.2280
 E  C  R  T  S  A  S  D  V  D  A  D  N  N  C  L  G  T  E  V         p.760

                                                                    g.32054
 GCTTAA                                                             c.2286
 A  X                                                               p.761

          .         .         .         .         .         .       g.32114
 actctaggcacaggccggggctgcggtgcaggcacctggccatgctggctgggcggccca       c.*60

          .         .         .         .         .         .       g.32174
 agcacagccctgactaggatgacagcagcacaaaagaccacctttctcccctgagaggag       c.*120

          .         .         .         .         .         .       g.32234
 cttctgctactctgcatcactgatgacactcagcagggtgatgcacagcagtctgcctcc       c.*180

          .         .         .         .         .         .       g.32294
 cctatgggactcccttctaccaagcacatgagctctctaacagggtgggggctaccccca       c.*240

          .         .         .         .         .         .       g.32354
 gacctgctcctacactgatattgaagaacctggagaggatccttcagttctggccattcc       c.*300

          .         .         .         .         .         .       g.32414
 agggaccctccagaaacacagtgtttcaagagaccctaaaaaacctgcctgtcccaggac       c.*360

          .         .         .         .         .         .       g.32474
 cctatggtaatgaacaccaaacatctaaacaatcatatgctaacatgccactcctggaaa       c.*420

          .         .         .         .         .         .       g.32534
 ctccactctgaagctgccgctttggacaccaacactcccttctcccagggtcatgcaggg       c.*480

          .         .         .         .         .         .       g.32594
 atctgctccctcctgcttcccttaccagtcgtgcaccgctgactcccaggaagtctttcc       c.*540

          .         .         .         .         .         .       g.32654
 tgaagtctgaccacctttcttcttgcttcagttggggcagactctgatcccttctgccct       c.*600

          .         .         .         .         .         .       g.32714
 ggcagaatggcaggggtaatctgagccttcttcactcctttaccctagctgaccccttca       c.*660

          .         .         .         .         .         .       g.32774
 cctctccccctcccttttcctttgttttgggattcagaaaactgcttgtcagagactgtt       c.*720

          .         .         .                                     g.32808
 tattttttattaaaaatataaggcttatgtatga                                 c.*754

 (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 Sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A 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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