class II, major histocompatibility complex, transactivator (CIITA) - coding DNA reference sequence

(used for mutation description)

(last modified April 30, 2014)


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

The sequence was taken from NC_000016.9, covering CIITA transcript NM_000246.3.


Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                                                   .                g.1013
                                                ggttagtgatgag       c.-121

 .         .         .         .         .         .                g.1073
 gctagtgatgaggctgtgtgcttctgagctgggcatccgaaggcatccttggggaagctg       c.-61

 .         .         .         .         .         .                g.1133
 agggcacgaggaggggctgccagactccgggagctgctgcctggctgggattcctacaca       c.-1

          .         .         .         .         .   | 02     .    g.19092
 ATGCGTTGCCTGGCTCCACGCCCTGCTGGGTCCTACCTGTCAGAGCCCCAAG | GCAGCTCA    c.60
 M  R  C  L  A  P  R  P  A  G  S  Y  L  S  E  P  Q  G |   S  S      p.20

          .         .         .         .         .         .       g.19152
 CAGTGTGCCACCATGGAGTTGGGGCCCCTAGAAGGTGGCTACCTGGAGCTTCTTAACAGC       c.120
 Q  C  A  T  M  E  L  G  P  L  E  G  G  Y  L  E  L  L  N  S         p.40

          .         .         .         .         .         .       g.19212
 GATGCTGACCCCCTGTGCCTCTACCACTTCTATGACCAGATGGACCTGGCTGGAGAAGAA       c.180
 D  A  D  P  L  C  L  Y  H  F  Y  D  Q  M  D  L  A  G  E  E         p.60

          .          | 03        .         .         .         .    g.19512
 GAGATTGAGCTCTACTCAG | AACCCGACACAGACACCATCAACTGCGACCAGTTCAGCAGG    c.240
 E  I  E  L  Y  S  E |   P  D  T  D  T  I  N  C  D  Q  F  S  R      p.80

          .         .         .         .         .      | 04  .    g.22477
 CTGTTGTGTGACATGGAAGGTGATGAAGAGACCAGGGAGGCTTATGCCAATATCG | CGGAA    c.300
 L  L  C  D  M  E  G  D  E  E  T  R  E  A  Y  A  N  I  A |   E      p.100

          .         .         .         .         .         | 05    g.22729
 CTGGACCAGTATGTCTTCCAGGACTCCCAGCTGGAGGGCCTGAGCAAGGACATTTTCA | AG    c.360
 L  D  Q  Y  V  F  Q  D  S  Q  L  E  G  L  S  K  D  I  F  K |       p.120

          .         .         .         .         .         .       g.22789
 CACATAGGACCAGATGAAGTGATCGGTGAGAGTATGGAGATGCCAGCAGAAGTTGGGCAG       c.420
 H  I  G  P  D  E  V  I  G  E  S  M  E  M  P  A  E  V  G  Q         p.140

          .       | 06 .         .         .         .         .    g.25360
 AAAAGTCAGAAAAGAC | CCTTCCCAGAGGAGCTTCCGGCAGACCTGAAGCACTGGAAGCCA    c.480
 K  S  Q  K  R  P |   F  P  E  E  L  P  A  D  L  K  H  W  K  P      p.160

   | 07      .         .         .         .         .         .    g.25899
 G | CTGAGCCCCCCACTGTGGTGACTGGCAGTCTCCTAGTGAGACCAGTGAGCGACTGCTCC    c.540
 A |   E  P  P  T  V  V  T  G  S  L  L  V  R  P  V  S  D  C  S      p.180

          .         .         .         .         .         .       g.25959
 ACCCTGCCCTGCCTGCCACTGCCTGCGCTGTTCAACCAGGAGCCAGCCTCCGGCCAGATG       c.600
 T  L  P  C  L  P  L  P  A  L  F  N  Q  E  P  A  S  G  Q  M         p.200

          .         .         | 08         .         .         .    g.26492
 CGCCTGGAGAAAACCGACCAGATTCCCA | TGCCTTTCTCCAGTTCCTCGTTGAGCTGCCTG    c.660
 R  L  E  K  T  D  Q  I  P  M |   P  F  S  S  S  S  L  S  C  L      p.220

          .         .         .         .         .         .       g.26552
 AATCTCCCTGAGGGACCCATCCAGTTTGTCCCCACCATCTCCACTCTGCCCCATGGGCTC       c.720
 N  L  P  E  G  P  I  Q  F  V  P  T  I  S  T  L  P  H  G  L         p.240

          .         .         .         .         .   | 09     .    g.27541
 TGGCAAATCTCTGAGGCTGGAACAGGGGTCTCCAGTATATTCATCTACCATG | GTGAGGTG    c.780
 W  Q  I  S  E  A  G  T  G  V  S  S  I  F  I  Y  H  G |   E  V      p.260

          .         .         .         .         .         .       g.27601
 CCCCAGGCCAGCCAAGTACCCCCTCCCAGTGGATTCACTGTCCACGGCCTCCCAACATCT       c.840
 P  Q  A  S  Q  V  P  P  P  S  G  F  T  V  H  G  L  P  T  S         p.280

          .         .         .         .         .         .       g.27661
 CCAGACCGGCCAGGCTCCACCAGCCCCTTCGCTCCATCAGCCACTGACCTGCCCAGCATG       c.900
 P  D  R  P  G  S  T  S  P  F  A  P  S  A  T  D  L  P  S  M         p.300

          .         .         .        | 10.         .         .    g.28569
 CCTGAACCTGCCCTGACCTCCCGAGCAAACATGACAG | AGCACAAGACGTCCCCCACCCAA    c.960
 P  E  P  A  L  T  S  R  A  N  M  T  E |   H  K  T  S  P  T  Q      p.320

          .         .         .         .       | 11 .         .    g.30315
 TGCCCGGCAGCTGGAGAGGTCTCCAACAAGCTTCCAAAATGGCCTG | AGCCGGTGGAGCAG    c.1020
 C  P  A  A  G  E  V  S  N  K  L  P  K  W  P  E |   P  V  E  Q      p.340

          .         .         .         .         .         .       g.30375
 TTCTACCGCTCACTGCAGGACACGTATGGTGCCGAGCCCGCAGGCCCGGATGGCATCCTA       c.1080
 F  Y  R  S  L  Q  D  T  Y  G  A  E  P  A  G  P  D  G  I  L         p.360

          .         .         .         .         .         .       g.30435
 GTGGAGGTGGATCTGGTGCAGGCCAGGCTGGAGAGGAGCAGCAGCAAGAGCCTGGAGCGG       c.1140
 V  E  V  D  L  V  Q  A  R  L  E  R  S  S  S  K  S  L  E  R         p.380

          .         .         .         .         .         .       g.30495
 GAACTGGCCACCCCGGACTGGGCAGAACGGCAGCTGGCCCAAGGAGGCCTGGCTGAGGTG       c.1200
 E  L  A  T  P  D  W  A  E  R  Q  L  A  Q  G  G  L  A  E  V         p.400

          .         .         .         .         .         .       g.30555
 CTGTTGGCTGCCAAGGAGCACCGGCGGCCGCGTGAGACACGAGTGATTGCTGTGCTGGGC       c.1260
 L  L  A  A  K  E  H  R  R  P  R  E  T  R  V  I  A  V  L  G         p.420

          .         .         .         .         .         .       g.30615
 AAAGCTGGTCAGGGCAAGAGCTATTGGGCTGGGGCAGTGAGCCGGGCCTGGGCTTGTGGC       c.1320
 K  A  G  Q  G  K  S  Y  W  A  G  A  V  S  R  A  W  A  C  G         p.440

          .         .         .         .         .         .       g.30675
 CGGCTTCCCCAGTACGACTTTGTCTTCTCTGTCCCCTGCCATTGCTTGAACCGTCCGGGG       c.1380
 R  L  P  Q  Y  D  F  V  F  S  V  P  C  H  C  L  N  R  P  G         p.460

          .         .         .         .         .         .       g.30735
 GATGCCTATGGCCTGCAGGATCTGCTCTTCTCCCTGGGCCCACAGCCACTCGTGGCGGCC       c.1440
 D  A  Y  G  L  Q  D  L  L  F  S  L  G  P  Q  P  L  V  A  A         p.480

          .         .         .         .         .         .       g.30795
 GATGAGGTTTTCAGCCACATCTTGAAGAGACCTGACCGCGTTCTGCTCATCCTAGACGGC       c.1500
 D  E  V  F  S  H  I  L  K  R  P  D  R  V  L  L  I  L  D  G         p.500

          .         .         .         .         .         .       g.30855
 TTCGAGGAGCTGGAAGCGCAAGATGGCTTCCTGCACAGCACGTGCGGACCGGCACCGGCG       c.1560
 F  E  E  L  E  A  Q  D  G  F  L  H  S  T  C  G  P  A  P  A         p.520

          .         .         .         .         .         .       g.30915
 GAGCCCTGCTCCCTCCGGGGGCTGCTGGCCGGCCTTTTCCAGAAGAAGCTGCTCCGAGGT       c.1620
 E  P  C  S  L  R  G  L  L  A  G  L  F  Q  K  K  L  L  R  G         p.540

          .         .         .         .         .         .       g.30975
 TGCACCCTCCTCCTCACAGCCCGGCCCCGGGGCCGCCTGGTCCAGAGCCTGAGCAAGGCC       c.1680
 C  T  L  L  L  T  A  R  P  R  G  R  L  V  Q  S  L  S  K  A         p.560

          .         .         .         .         .         .       g.31035
 GACGCCCTATTTGAGCTGTCCGGCTTCTCCATGGAGCAGGCCCAGGCATACGTGATGCGC       c.1740
 D  A  L  F  E  L  S  G  F  S  M  E  Q  A  Q  A  Y  V  M  R         p.580

          .         .         .         .         .         .       g.31095
 TACTTTGAGAGCTCAGGGATGACAGAGCACCAAGACAGAGCCCTGACGCTCCTCCGGGAC       c.1800
 Y  F  E  S  S  G  M  T  E  H  Q  D  R  A  L  T  L  L  R  D         p.600

          .         .         .         .         .         .       g.31155
 CGGCCACTTCTTCTCAGTCACAGCCACAGCCCTACTTTGTGCCGGGCAGTGTGCCAGCTC       c.1860
 R  P  L  L  L  S  H  S  H  S  P  T  L  C  R  A  V  C  Q  L         p.620

          .         .         .         .         .         .       g.31215
 TCAGAGGCCCTGCTGGAGCTTGGGGAGGACGCCAAGCTGCCCTCCACGCTCACGGGACTC       c.1920
 S  E  A  L  L  E  L  G  E  D  A  K  L  P  S  T  L  T  G  L         p.640

          .         .         .         .         .         .       g.31275
 TATGTCGGCCTGCTGGGCCGTGCAGCCCTCGACAGCCCCCCCGGGGCCCTGGCAGAGCTG       c.1980
 Y  V  G  L  L  G  R  A  A  L  D  S  P  P  G  A  L  A  E  L         p.660

          .         .         .         .         .         .       g.31335
 GCCAAGCTGGCCTGGGAGCTGGGCCGCAGACATCAAAGTACCCTACAGGAGGACCAGTTC       c.2040
 A  K  L  A  W  E  L  G  R  R  H  Q  S  T  L  Q  E  D  Q  F         p.680

          .         .         .         .         .         .       g.31395
 CCATCCGCAGACGTGAGGACCTGGGCGATGGCCAAAGGCTTAGTCCAACACCCACCGCGG       c.2100
 P  S  A  D  V  R  T  W  A  M  A  K  G  L  V  Q  H  P  P  R         p.700

          .         .         .         .         .         .       g.31455
 GCCGCAGAGTCCGAGCTGGCCTTCCCCAGCTTCCTCCTGCAATGCTTCCTGGGGGCCCTG       c.2160
 A  A  E  S  E  L  A  F  P  S  F  L  L  Q  C  F  L  G  A  L         p.720

          .         .         .         .         .         .       g.31515
 TGGCTGGCTCTGAGTGGCGAAATCAAGGACAAGGAGCTCCCGCAGTACCTAGCATTGACC       c.2220
 W  L  A  L  S  G  E  I  K  D  K  E  L  P  Q  Y  L  A  L  T         p.740

          .         .         .         .         .         .       g.31575
 CCAAGGAAGAAGAGGCCCTATGACAACTGGCTGGAGGGCGTGCCACGCTTTCTGGCTGGG       c.2280
 P  R  K  K  R  P  Y  D  N  W  L  E  G  V  P  R  F  L  A  G         p.760

          .         .         .         .         .         .       g.31635
 CTGATCTTCCAGCCTCCCGCCCGCTGCCTGGGAGCCCTACTCGGGCCATCGGCGGCTGCC       c.2340
 L  I  F  Q  P  P  A  R  C  L  G  A  L  L  G  P  S  A  A  A         p.780

          .         .         .         .         .         .       g.31695
 TCGGTGGACAGGAAGCAGAAGGTGCTTGCGAGGTACCTGAAGCGGCTGCAGCCGGGGACA       c.2400
 S  V  D  R  K  Q  K  V  L  A  R  Y  L  K  R  L  Q  P  G  T         p.800

          .         .         .         .         .         .       g.31755
 CTGCGGGCGCGGCAGCTGCTGGAGCTGCTGCACTGCGCCCACGAGGCCGAGGAGGCTGGA       c.2460
 L  R  A  R  Q  L  L  E  L  L  H  C  A  H  E  A  E  E  A  G         p.820

          .         .         .         .         .         .       g.31815
 ATTTGGCAGCACGTGGTACAGGAGCTCCCCGGCCGCCTCTCTTTTCTGGGCACCCGCCTC       c.2520
 I  W  Q  H  V  V  Q  E  L  P  G  R  L  S  F  L  G  T  R  L         p.840

          .         .         .         .         .         .       g.31875
 ACGCCTCCTGATGCACATGTACTGGGCAAGGCCTTGGAGGCGGCGGGCCAAGACTTCTCC       c.2580
 T  P  P  D  A  H  V  L  G  K  A  L  E  A  A  G  Q  D  F  S         p.860

          .         .         .         .         .         .       g.31935
 CTGGACCTCCGCAGCACTGGCATTTGCCCCTCTGGATTGGGGAGCCTCGTGGGACTCAGC       c.2640
 L  D  L  R  S  T  G  I  C  P  S  G  L  G  S  L  V  G  L  S         p.880

          .        | 12.         .         .         .         .    g.32874
 TGTGTCACCCGTTTCAG | GGCTGCCTTGAGCGACACGGTGGCGCTGTGGGAGTCCCTGCAG    c.2700
 C  V  T  R  F  R  |  A  A  L  S  D  T  V  A  L  W  E  S  L  Q      p.900

          .         .         .         .         .         .       g.32934
 CAGCATGGGGAGACCAAGCTACTTCAGGCAGCAGAGGAGAAGTTCACCATCGAGCCTTTC       c.2760
 Q  H  G  E  T  K  L  L  Q  A  A  E  E  K  F  T  I  E  P  F         p.920

          .         .         .         .         .       | 13 .    g.33994
 AAAGCCAAGTCCCTGAAGGATGTGGAAGACCTGGGAAAGCTTGTGCAGACTCAGAG | GACG    c.2820
 K  A  K  S  L  K  D  V  E  D  L  G  K  L  V  Q  T  Q  R  |  T      p.940

          .         .         .         .         .         .       g.34054
 AGAAGTTCCTCGGAAGACACAGCTGGGGAGCTCCCTGCTGTTCGGGACCTAAAGAAACTG       c.2880
 R  S  S  S  E  D  T  A  G  E  L  P  A  V  R  D  L  K  K  L         p.960

          | 14         .         .         .         .         .    g.39424
 GAGTTTGC | GCTGGGCCCTGTCTCAGGCCCCCAGGCTTTCCCCAAACTGGTGCGGATCCTC    c.2940
 E  F  A  |  L  G  P  V  S  G  P  Q  A  F  P  K  L  V  R  I  L      p.980

          .         .          | 15        .         .         .    g.40200
 ACGGCCTTTTCCTCCCTGCAGCATCTGGA | CCTGGATGCGCTGAGTGAGAACAAGATCGGG    c.3000
 T  A  F  S  S  L  Q  H  L  D  |  L  D  A  L  S  E  N  K  I  G      p.1000

          .         .         .         .         .         .       g.40260
 GACGAGGGTGTCTCGCAGCTCTCAGCCACCTTCCCCCAGCTGAAGTCCTTGGAAACCCTC       c.3060
 D  E  G  V  S  Q  L  S  A  T  F  P  Q  L  K  S  L  E  T  L         p.1020

    | 16     .         .         .         .         .         .    g.42300
 AA | TCTGTCCCAGAACAACATCACTGACCTGGGTGCCTACAAACTCGCCGAGGCCCTGCCT    c.3120
 N  |  L  S  Q  N  N  I  T  D  L  G  A  Y  K  L  A  E  A  L  P      p.1040

          .         .          | 17        .         .         .    g.46000
 TCGCTCGCTGCATCCCTGCTCAGGCTAAG | CTTGTACAATAACTGCATCTGCGACGTGGGA    c.3180
 S  L  A  A  S  L  L  R  L  S  |  L  Y  N  N  C  I  C  D  V  G      p.1060

          .         .         .         .         .    | 18    .    g.46216
 GCCGAGAGCTTGGCTCGTGTGCTTCCGGACATGGTGTCCCTCCGGGTGATGGA | CGTCCAG    c.3240
 A  E  S  L  A  R  V  L  P  D  M  V  S  L  R  V  M  D  |  V  Q      p.1080

          .         .         .         .         .         .       g.46276
 TACAACAAGTTCACGGCTGCCGGGGCCCAGCAGCTCGCTGCCAGCCTTCGGAGGTGTCCT       c.3300
 Y  N  K  F  T  A  A  G  A  Q  Q  L  A  A  S  L  R  R  C  P         p.1100

          .        | 19.         .         .         .         .    g.47073
 CATGTGGAGACGCTGGC | GATGTGGACGCCCACCATCCCATTCAGTGTCCAGGAACACCTG    c.3360
 H  V  E  T  L  A  |  M  W  T  P  T  I  P  F  S  V  Q  E  H  L      p.1120

          .         .         .                                 g.47106
 CAACAACAGGATTCACGGATCAGCCTGAGATGA |                               c.3394
 Q  Q  Q  D  S  R  I  S  L  R  X                                 p.1130

          .         .   | 20     .         .         .         .    g.47718
 tcccagctgtgctctggacagg | catgttctctgaggacactaaccacgctggaccttgaa    c.*60

          .         .         .         .         .         .       g.47778
 ctgggtacttgtggacacagctcttctccaggctgtatcccatgagcctcagcatcctgg       c.*120

          .         .         .         .         .         .       g.47838
 cacccggcccctgctggttcagggttggcccctgcccggctgcggaatgaaccacatctt       c.*180

          .         .         .         .         .         .       g.47898
 gctctgctgacagacacaggcccggctccaggctcctttagcgcccagttgggtggatgc       c.*240

          .         .         .         .         .         .       g.47958
 ctggtggcagctgcggtccacccaggagccccgaggccttctctgaaggacattgcggac       c.*300

          .         .         .         .         .         .       g.48018
 agccacggccaggccagagggagtgacagaggcagccccattctgcctgcccaggcccct       c.*360

          .         .         .         .         .         .       g.48078
 gccaccctggggagaaagtacttctttttttttatttttagacagagtctcactgttgcc       c.*420

          .         .         .         .         .         .       g.48138
 caggctggcgtgcagtggtgcgatctgggttcactgcaacctccgcctcttgggttcaag       c.*480

          .         .         .         .         .         .       g.48198
 cgattcttctgcttcagcctcccgagtagctgggactacaggcacccaccatcatgtctg       c.*540

          .         .         .         .         .         .       g.48258
 gctaatttttcatttttagtagagacagggttttgccatgttggccaggctggtctcaaa       c.*600

          .         .         .         .         .         .       g.48318
 ctcttgacctcaggtgatccacccacctcagcctcccaaagtgctgggattacaagcgtg       c.*660

          .         .         .         .         .         .       g.48378
 agccactgcaccgggccacagagaaagtacttctccaccctgctctccgaccagacacct       c.*720

          .         .         .         .         .         .       g.48438
 tgacagggcacaccgggcactcagaagacactgatgggcaacccccagcctgctaattcc       c.*780

          .         .         .         .         .         .       g.48498
 ccagattgcaacaggctgggcttcagtggcagctgcttttgtctatgggactcaatgcac       c.*840

          .         .         .         .         .         .       g.48558
 tgacattgttggccaaagccaaagctaggcctggccagatgcaccagcccttagcaggga       c.*900

          .         .         .         .         .         .       g.48618
 aacagctaatgggacactaatggggcggtgagaggggaacagactggaagcacagcttca       c.*960

          .         .         .         .         .         .       g.48678
 tttcctgtgtcttttttcactacattataaatgtctctttaatgtcacaggcaggtccag       c.*1020

          .         .         .         .         .         .       g.48738
 ggtttgagttcataccctgttaccattttggggtacccactgctctggttatctaatatg       c.*1080

          .         .         .         .                           g.48786
 taacaagccaccccaaatcatagtggcttaaaacaacactcacattta                   c.*1128

 (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 Class II, major histocompatibility complex, transactivator 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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