Sarcospan (SSPN) - coding DNA reference sequence

(used for mutation description)

(last modified January 2, 2011)


This file was created to facilitate the description of sequence variants in the SSPN gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_012011.1, covering SSPN transcript variant-1 (NM_005086.4).  The SSPN gene uses an alternative promoter/exon 01b in the 5' upstream region generating SSPN transcript variant- 2 (NM_001135823.1), encoding the shorter protein isoform 2 (translation start in exon 2).

Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                     .         .         .         .                g.5277
                     ataattcgaataccagggcaggccgagccagccgtgcgcc       c.-61

 .         .         .         .         .         .                g.5337
 gcgctccagggcccagggcgccgcacacgcacccacccacccacccagcctcgcagcgcc       c.-1

          .         .         .         .         .         .       g.5397
 ATGGGCAAGAACAAGCAGCCACGCGGCCAGCAGAGGCAGGGGGGCCCGCCGGCCGCGGAC       c.60
 M  G  K  N  K  Q  P  R  G  Q  Q  R  Q  G  G  P  P  A  A  D         p.20

          .         .         .         .         .         .       g.5457
 GCCGCTGGGCCCGACGACATGGAGCCGAAGAAGGGCACGGGGGCCCCCAAGGAGTGCGGG       c.120
 A  A  G  P  D  D  M  E  P  K  K  G  T  G  A  P  K  E  C  G         p.40

          .         .         .         .         .         .       g.5517
 GAGGAGGAGCCCCGGACCTGCTGCGGCTGCCGGTTCCCGCTGCTGCTCGCCCTGCTGCAG       c.180
 E  E  E  P  R  T  C  C  G  C  R  F  P  L  L  L  A  L  L  Q         p.60

          .         .         .         .         .         .       g.5577
 CTGGCCCTGGGCATCGCCGTGACCGTGGTGGGCTTCCTCATGGCGAGCATCAGCTCCTCC       c.240
 L  A  L  G  I  A  V  T  V  V  G  F  L  M  A  S  I  S  S  S         p.80

          .         .         .          | 02        .         .    g.33978
 CTGCTAGTCAGGGACACTCCATTTTGGGCTGGGATCATT | GTCTGCTTAGTGGCCTATCTT    c.300
 L  L  V  R  D  T  P  F  W  A  G  I  I   | V  C  L  V  A  Y  L      p.100

          .         .         .         .         .         .       g.34038
 GGCTTGTTTATGCTTTGTGTCTCATATCAGGTTGACGAACGGACATGTATTCAATTTTCT       c.360
 G  L  F  M  L  C  V  S  Y  Q  V  D  E  R  T  C  I  Q  F  S         p.120
          ^ translation start SSPN isoform 2

        | 03 .         .         .         .         .         .    g.40429
 ATGAAA | CTGTTATACTTTCTGCTGAGTGCCCTGGGCCTGACGGTCTGTGTGCTGGCCGTG    c.420
 M  K   | L  L  Y  F  L  L  S  A  L  G  L  T  V  C  V  L  A  V      p.140

          .         .         .         .         .         .       g.40489
 GCCTTTGCCGCCCACCACTATTCGCAGCTCACACAGTTTACCTGTGAGACCACACTCGAC       c.480
 A  F  A  A  H  H  Y  S  Q  L  T  Q  F  T  C  E  T  T  L  D         p.160

          .         .         .         .         .         .       g.40549
 TCTTGCCAGTGCAAACTGCCCTCCTCGGAGCCGCTCAGCAGGACCTTTGTTTACCGGGAT       c.540
 S  C  Q  C  K  L  P  S  S  E  P  L  S  R  T  F  V  Y  R  D         p.180

          .         .         .         .         .         .       g.40609
 GTGACGGACTGTACCAGCGTCACTGGCACTTTCAAACTGTTCTTACTCATCCAGATGATT       c.600
 V  T  D  C  T  S  V  T  G  T  F  K  L  F  L  L  I  Q  M  I         p.200

          .         .         .         .         .         .       g.40669
 CTTAATTTGGTCTGCGGCCTTGTGTGCTTGTTGGCCTGCTTTGTGATGTGGAAACATAGG       c.660
 L  N  L  V  C  G  L  V  C  L  L  A  C  F  V  M  W  K  H  R         p.220

          .         .         .         .         .         .       g.40729
 TACCAGGTCTTCTATGTGGGTGTCAGGATATGCTCCCTCACGGCTTCCGAAGGCCCCCAG       c.720
 Y  Q  V  F  Y  V  G  V  R  I  C  S  L  T  A  S  E  G  P  Q         p.240

          .                                                         g.40741
 CAAAAGATCTAA                                                       c.732
 Q  K  I  X                                                         p.243

          .         .         .         .         .         .       g.40801
 cattcttgctcaaagttgcgagagaaagtagcacatggagtagctgaggttaaacaaaca       c.*60

          .         .         .         .         .         .       g.40861
 aaaaaaaattttaaacaaagaaaggaaaaaaattgacaataaaagtcactcttctaattg       c.*120

          .         .         .         .         .         .       g.40921
 aatatttttatatttttatgaaacaaaagagcatttcttcaggtttctattgtatttttt       c.*180

          .         .         .         .         .         .       g.40981
 ttaacattcttgcagagaaagcaagatccaaattgattttgggatattaaaagttaacag       c.*240

          .         .         .         .         .         .       g.41041
 aacactgaacaaggaaagaatggcatagatctatctttacagtctggagttaattcctgt       c.*300

          .         .         .         .         .         .       g.41101
 taactcattttatccattccttacataatcttctttcctgttagtccagtttgatggtgt       c.*360

          .         .         .         .         .         .       g.41161
 gaatggtgaatttcaggcccagttgctaaattttgtggcatcttcctctagtccttccca       c.*420

          .         .         .         .         .         .       g.41221
 cctccagtcatcagccccactctgtcttggagacaggcaggaggtgggggaagagctgaa       c.*480

          .         .         .         .         .         .       g.41281
 tctctttattttccctggtagagacatcttcaaggcatgaaatagcttaaagagcagagt       c.*540

          .         .         .         .         .         .       g.41341
 agaaacggaagaggctttgcaaaaggctagataactaacaacacctgggttggggcggcg       c.*600

          .         .         .         .         .         .       g.41401
 gcctcttctcttcagctcccttagcttggctccgtaagtggatcacttgccaaatgcttt       c.*660

          .         .         .         .         .         .       g.41461
 agatgattgcctctcaataattgaaaggtggtggtagttgtattctaaatgatgtagaag       c.*720

          .         .         .         .         .         .       g.41521
 gtttaaaaataattacattatgcttctattctatcatctaaaacaaatcattaaaactaa       c.*780

          .         .         .         .         .         .       g.41581
 tttctagctaattgttaattataattatgctcagaagtctatttaatgagctctgactgt       c.*840

          .         .         .         .         .         .       g.41641
 acttacgctgcactgtcggtgttaagagaaattactctcacaagagcagaggcctgaaga       c.*900

          .         .         .         .         .         .       g.41701
 ttctttcttctgaaagccaagcaccacaaggaaaaaaaaaattattaatagctcaggtta       c.*960

          .         .         .         .         .         .       g.41761
 aaaacacccatttaaacaaaaacaagagcatttgtaataggaagtgtttatacaaacagc       c.*1020

          .         .         .         .         .         .       g.41821
 acatttgtgatatgttgaaaagcatctctcttggcaaccaatctatgtttgaggaagatt       c.*1080

          .         .         .         .         .         .       g.41881
 gggtaatgctgatgtgttccattcatgaaactgtatttgatacataatcctattattaat       c.*1140

          .         .         .         .         .         .       g.41941
 tcgtatgcttagtcaacctaggaaatcaaaataatgttttgaagttcttatttgagcaat       c.*1200

          .         .         .         .         .         .       g.42001
 atggccttgacttggagggtagttttagttgttttgtttttaagtgactgtggtttaaag       c.*1260

          .         .         .         .         .         .       g.42061
 cacaaatgccccaaggtggggagacttctctctgtgattattgttgctattaaattctga       c.*1320

          .         .         .         .         .         .       g.42121
 actgtatccatattttaaggaaggagctaaaaatggaaattcatgaaacataaatggtat       c.*1380

          .         .         .         .         .         .       g.42181
 caagaactttatcagtatgctttgttgaaagcagaaattaagataataattgagttcaat       c.*1440

          .         .         .         .         .         .       g.42241
 tcgcctctccgcattgcctattgatacactttactaatcatgaaattctaacctaaaagg       c.*1500

          .         .         .         .         .         .       g.42301
 aaaacattttcctgcttgtcttagaagaaagtggaataattccactgattgtgataatgg       c.*1560

          .         .         .         .         .         .       g.42361
 tttcaatttctacacaatataaatatccagtataaaggaaagcgttaagtcggtaagcta       c.*1620

          .         .         .         .         .         .       g.42421
 gaggattgtaaatatcttttatgtcctctagataaaacacccgattaacagatgttaaac       c.*1680

          .         .         .         .         .         .       g.42481
 cttttaatgttttgatttgctttaaaaatggccttcctacacattagctccagctaaaaa       c.*1740

          .         .         .         .         .         .       g.42541
 gacacattggagagcttagaggataagtctctggagcagaatttatcacacacaaaagtt       c.*1800

          .         .         .         .         .         .       g.42601
 acaccaacagaataccaagcagaatgatgaggacctgtaaaataccttgtgccctattaa       c.*1860

          .         .         .         .         .         .       g.42661
 aaaaaaaaaaaaaaaaaaagccagtaactgaatccattttgatttttggttgagtttcct       c.*1920

          .         .         .         .         .         .       g.42721
 acacaaagaagaaaataactgagaatctggaatgttgtagtccatcctttaaagagtaag       c.*1980

          .         .         .         .         .         .       g.42781
 aaagtagcagttaatgctagtaaccgtgaattaggcaccactgaaagcacatcccgaatt       c.*2040

          .         .         .         .         .         .       g.42841
 tctttaacaacaacattttatagtgaacactacaagtttttatatttaaaaattaagact       c.*2100

          .         .         .         .         .         .       g.42901
 ctgtatatccttaaggtgctctatgctttaccagtaattcacagggtatttcaaatggta       c.*2160

          .         .         .         .         .         .       g.42961
 gaatcattttagcttctgtgcttcctttttctaaataatgcaacttgtaagagttgacat       c.*2220

          .         .         .         .         .         .       g.43021
 tgtaataagctttataatagtataaccgtcaggagatatatatatatatatatacacata       c.*2280

          .         .         .         .         .         .       g.43081
 cacacacacacacacatatatactatacatatataaaatggggatattactattgtatga       c.*2340

          .         .         .         .         .         .       g.43141
 ttaaatcattcttaagtccccaaggaaaaaaaatcataaacaaatagaaagaactaaaca       c.*2400

          .         .         .         .         .         .       g.43201
 gaaaagaaagaaagaaaagatccctttgctatgagctcgctgtatattgataagtgtaag       c.*2460

          .         .         .         .         .         .       g.43261
 aattgtgttgcatgaataaccgctttgggctggatttgaagtattttgatgttgtgtttt       c.*2520

          .         .         .         .         .         .       g.43321
 gcaaatattgaagttacaataatggcaacagaaaaggaacagatacacagctttacactt       c.*2580

          .         .         .         .         .         .       g.43381
 agcagaatgttacatttaaaatctgacaaggcgccaagatggtgactgtctcctctaaac       c.*2640

          .         .         .         .         .         .       g.43441
 cacgaaagagtaagatttgtgcaaccctcctcctcttccacctccttcaggagaattaaa       c.*2700

          .         .         .         .         .         .       g.43501
 tgaatcaagactttggaaagacggggaagagccgggacttggcagtacttgaaacaggag       c.*2760

          .         .         .         .         .         .       g.43561
 gaatacaccagcctaaatgtacagactttgtagccgagcccactcgatcggtctgtgcct       c.*2820

          .         .         .         .         .         .       g.43621
 tcacgtgaccaccatctgtgcctccctcgctccatccaaatttgtgtaggctgctccttg       c.*2880

          .         .         .         .         .         .       g.43681
 gagctatgcctaaaatatagctacaccagagccctggaaactgtagtcaagtaacaggcc       c.*2940

          .         .         .         .         .         .       g.43741
 tcactgttttttttctttggattaaaagtgtatatctctctactgaggggtttccagctt       c.*3000

          .         .         .         .         .         .       g.43801
 tacacttctataggttgttctgacagtgagaacacattatgtacatgttttctattcatg       c.*3060

          .         .         .         .         .         .       g.43861
 tccagggcatgagaatcttaatattcttatacttccctttttgcatgcagtatgtctgga       c.*3120

          .         .         .         .         .         .       g.43921
 atatgtttataaaattttagcaaggggtgagatcaagggacaaaggtagagtggttattt       c.*3180

          .         .         .         .         .         .       g.43981
 aaagacaatcagaaatgaacttaaaagctgccctgcaaaaccaatcctttcctatcatga       c.*3240

          .         .         .         .         .         .       g.44041
 agagtaccttcatattttctagagattgtctctgaaccgttgctacatagccataaattt       c.*3300

          .         .         .         .         .         .       g.44101
 ctgtaaatcatgttggctatcagttcttgctattctcagagcactctatcatgtttttag       c.*3360

          .         .         .         .         .         .       g.44161
 gtgtatattgtgtattcaggatagcattaaaaagaactgatggcaaatgtattgactcac       c.*3420

          .         .         .         .         .         .       g.44221
 agtggaaacattcatttggatgaagaattagtggtttagcctttgaaatgaataccttga       c.*3480

          .         .         .         .         .         .       g.44281
 atcatttcttctgattttctagtagtttattatctcaaatgattattatccccttcaaaa       c.*3540

          .         .         .         .         .         .       g.44341
 atactggtctgtactttggtgttgtggtttcatttttctggcattgatcaaatagcaaat       c.*3600

          .         .         .         .         .         .       g.44401
 acaaaataaagcatttctacatgtttgaggtggttgtttttaaaggggatatgtgtaatg       c.*3660

          .         .         .         .                           g.44442
 cagattttctttattaataaaattttcataatctctgaaaa                          c.*3701

 (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 Sarcospan 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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