Alignment of alleles: Human TRAC

The nucleotide between parentheses at the beginning of exons comes from a DONOR-SPLICE (n from ngt). The first nucleotide from an INT-DONOR-SPLICE is underlined (n from ngt).

Exon names are shown between parentheses on the first line.
Cysteine involved in the disulfide bridge are shown in purple.
STOP-CODON is indicated by an asterisk.

When several alleles are shown, the nucleotide mutations and amino acid changes for a given codon are indicated in red letters.
Dashes indicate identical nucleotides. Dots indicate gaps by comparison to the longest sequence. Blanks indicate partial sequences (blanks at the 5' and/or 3' end).

importantFirst codon and amino acid at position 1.3 depends on the last nucleotide of the TRA J-REGION (Alignment of alleles: Human (Homo sapiens) TRAJ). This amino acid may be an N (aat), H (cat), D (gat) or Y (tat).

                                                                                                               
                                                                1.3 1.2 1.1   1   2   3   4   5   6   7   8   9  10  11
                                                                 N   I   Q   N   P   D   P   A   V   Y   Q   L   R   D 
  X02883  ,TRAC*01 (EX1)                                      (A)AT ATC CAG AAC CCT GAC CCT GCC GTG TAC CAG CTG AGA GAC
                                                                                                               
  X02592  ,TRAC*01,(cDNA)                                     (-)-- --- --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  M14858  ,TRAC*01                                            (-)-- --- --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                                  
  AE000662,TRAC*01                                            (-)-- --- --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  M94081  ,TRAC*01                                            (-)-- --- --- --- --- --- --- --- --- --- --- --- --- ---

                                                        ___AB_______                                            ________
                                                       15.1    15.3                                                    
                                         12  13  14  15    15.2      16  17  18  19  20  21  22  23  24  25  26  27  28
                                         S   K                           S   S   D   K   S   V   C   L   F   T   D   F 
  X02883  ,TRAC*01 (EX1)                TCT AAA ... ... ... ... ... ... TCC AGT GAC AAG TCT GTC TGC CTA TTC ACC GAT TTT
                                                                                                               
  X02592  ,TRAC*01,(cDNA)               --- --- ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  M14858  ,TRAC*01                      --- --- ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  AE000662,TRAC*01                      --- --- ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  M94081  ,TRAC*01                      --- --- ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- ---

                                        _________BC_____________________                            ___________CD_______
                                                                                                   45.1    45.3    45.5
                                         29  30  31  32  33  34  35  36  39  40  41  42  43  44  45    45.2    45.4    
                                         D   S               Q   T   N   V   S   Q   S   K   D   S                     
  X02883  ,TRAC*01 (EX1)                GAT TCT ... ... ... CAA ACA AAT GTG TCA CAA AGT AAG GAT TCT ... ... ... ... ...
                                                                                                               
  X02592  ,TRAC*01,(cDNA)               --- --- ... ... ... --- --- --- --- --- --- --- --- --- --- ... ... ... ... ...
                                                                                                               
  M14858  ,TRAC*01                      --- --- ... ... ... --- --- --- --- --- --- --- --- --- --- ... ... ... ... ...
                                                                                                               
  AE000662,TRAC*01                      --- --- ... ... ... --- --- --- --- --- --- --- --- --- --- ... ... ... ... ...
                                                                                                               
  M94081  ,TRAC*01                      --- --- ... ... ... --- --- --- --- --- --- --- --- --- --- ... ... ... ... ...

                                       ________                                _________________________DE_____________
                                           45.7                                84.1    84.3    84.5    84.7    85.6    
                                       45.6      77  78  79  80  81  82  83  84    84.2    84.4    84.6    85.7    85.5
                                                 D   V   Y   I   T   D   K   T   V   L   D   M   R   S           M   D    
  X02883  ,TRAC*01 (EX1)                ... ... GAT GTG TAT ATC ACA GAC AAA ACT GTG CTA GAC ATG AGG TCT ... ... ATG GAC 
                                                                                                               
  X02592  ,TRAC*01,(cDNA)               ... ... --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... --- ---
                                                                                                               
  M14858  ,TRAC*01                      ... ... --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... --- ---
                                                                                                               
  AE000662,TRAC*01                      ... ... --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... --- ---
                                                                                                               
  M94081  ,TRAC*01                      ... ... --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... --- ---

                                       ________________                                                _EF_____        
                                       85.4    85.2                                                    96.1            
                                           85.3    85.1  85  86  87  88  89  90  91  92  93  94  95  96    96.2  97  98
                                         F   K   S   N   S   A   V   A   W   S   N   K   S                                 
  X02883  ,TRAC*01 (EX1)                TTC AAG AGC AAC AGT GCT GTG GCC TGG AGC AAC AAA TCT ... ... ... ... ... ... ...
                                                                                                               
  X02592  ,TRAC*01,(cDNA)               --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ...
                                                                                                               
  M14858  ,TRAC*01                      --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ...
                                                                                                               
  AE000662,TRAC*01                      --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ...
                                                                                                               
  M94081  ,TRAC*01                      --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ...

                                                                _______________________FG___________________________    
                                                                                                               
                                         99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118
                                                 D   F   A   C   A   N   A   F   N   N           S   I   I   P   E   D 
  X02883  ,TRAC*01 (EX1)                ... ... GAC TTT GCA TGT GCA AAC GCC TTC AAC AAC ... ... AGC ATT ATT CCA GAA GAC
                                                                                                               
  X02592  ,TRAC*01,(cDNA)               ... ... --- --- --- --- --- --- --- --- --- --- ... ... --- --- --- --- --- ---
                                                                                                               
  M14858  ,TRAC*01                      ... ... --- --- --- --- --- --- --- --- --- --- ... ... --- --- --- --- --- ---
                                                                                                               
  AE000662,TRAC*01                      ... ... --- --- --- --- --- --- --- --- --- --- ... ... --- --- --- --- --- ---
                                                                                                               
  M94081  ,TRAC*01                      ... ... --- --- --- --- --- --- --- --- --- --- ... ... --- --- --- --- --- ---

                                                       
                                        119 120 121 122 123 124
                                         T   F   F   P   S   P  
  X02883  ,TRAC*01 (EX1)                ACC TTC TTC CCC AGC CCA G
                                                        
  X02592  ,TRAC*01,(cDNA)               --- --- --- --- --- --- -
                                                        
  M14858  ,TRAC*01                      --- --- --- --- --- --- -
                                                        
  AE000662,TRAC*01                      --- --- --- --- --- --- -
                                                        
  M94081  ,TRAC*01                      --- --- --- --- --- --- -



                                          1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
                                         E   S   S   C   D   V   K   L   V   E   K   S   F   E   T  
  X02883  ,TRAC*01 (EX2)                 AA AGT TCC TGT GAT GTC AAG CTG GTC GAG AAA AGC TTT GAA ACA G
                                                                                            
  X02592  ,TRAC*01,(cDNA)                -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -
                                                                                            
  M14859  ,TRAC*01                       -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -
                                                                                            
  AE000662,TRAC*01                       -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -
                                                                                            
  M94081  ,TRAC*01                       -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -



                                          1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20
                                         D   T   N   L   N   F   Q   N   L   S   V   I   G   F   R   I   L   L   L   K 
  X02883  ,TRAC*01 (EX3)                 AT ACG AAC CTA AAC TTT CAA AAC CTG TCA GTG ATT GGG TTC CGA ATC CTC CTC CTG AAA
                                                                                                               
  X02592  ,TRAC*01,(cDNA)                -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  M14860  ,TRAC*01                       -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  AE000662,TRAC*01                       -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
                                                                                                               
  M94081  ,TRAC*01                       -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---

                                         21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
                                         V   A   G   F   N   L   L   M   T   L   R   L   W   S   S   *  
  X02883  ,TRAC*01 (EX3)                GTG GCC GGG TTT AAT CTG CTC ATG ACG CTG CGG CTG TGG TCC AGC TGA G
                                                                                                
  X02592  ,TRAC*01,(cDNA)               --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -
                                                                                                
  M14860  ,TRAC*01                      --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -
                                                                                                
  AE000662,TRAC*01                      --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -
                                                                                                
  M94081  ,TRAC*01                      --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -


  
  X02883  ,TRAC*01  (Untranslated EX4   ATCTGCAAGATTGTAAGACAGCCTGTGCTCCCTCGCTCCTTCCTCTGCATTGCCCCTCTTCTCCCTCTCCAAACAGAGG
                        and 3'UTR) 
  X02592  ,TRAC*01  (cDNA)              -------------------------------------------------------------------------------

  M14861,TRAC*01                        -------------------------------------------------------------------------------

  AE000662,TRAC*01                      -------------------------------------------------------------------------------

  M94081  ,TRAC*01                      -------------------------------------------------------------------------------
 
X02883 ,TRAC*01 GAACTCTCCCACCCCCAAGGAGGTGAAAGCTGCTACCACCTCTGTGCCCCCCCGC-AATGCCACCAACTGGATGGGATCC 160 # # # X02592 ,TRAC*01 ---------T--------------------------------------------GT-----------------.....-- # # # M14861,TRAC*01 ---------T--------------------------------------------GC-----------------.....-- # # # # AE000662,TRAC*01 ---------T--------------------------------------------GC-----.-----------.....-- # # # # M94081 ,TRAC*01 ---------T--------------------------------------------GC-----.-----------.....--
X02883 ,TRAC*01 TACCCGAATTTATGATTAAGATTGCTGAAGAGCTGCCAAACACTGCTGCCACCCCCTCTGTTCCCTTATTGCTGCTTGTC X02592 ,TRAC*01 -------------------------------------------------------------------------------- M14861,TRAC*01 -------------------------------------------------------------------------------- AE000662,TRAC*01 -------------------------------------------------------------------------------- M94081 ,TRAC*01 --------------------------------------------------------------------------------
X02883 ,TRAC*01 ACTGCCTGACATTCACGGCAGAGGCAAGGCTGCTGCAGCCTCCCCTGGCTGTGCACATTCCCTCCTGCTCCCCAGAGACT 320 X02592 ,TRAC*01 -------------------------------------------------------------------------------- M14861,TRAC*01 -------------------------------------------------------------------------------- # AE000662,TRAC*01 ---------------------------------------.---G------------------------------------ # M94081 ,TRAC*01 ---------------------------------------.---G------------------------------------
X02883 ,TRAC*01 GCCTCCGCCATCCCACAGATGATGGATCTTCAGTGGGTTCTCTTGGGCTCTAGGTCCTGGAGAATGTTGTGAGGG-TTTA # X02592 ,TRAC*01 ---------------------------------------------------------------------------G---- # M14861,TRAC*01 ---------------------------------------------------------------------------G---- # AE000662,TRAC*01 ---------------------------------------------------------C-----------------G---- # M94081 ,TRAC*01 ---------------------------------------------------------C-----------------G----
X02883 ,TRAC*01 TTTTTTTTTAATAGTGTTCATAAAGAAATACATAGTATTCTTCTTCTCAAGACGTGGGGGGAAATTATCTCATTATCGAG 480 X02592 ,TRAC*01 -------------------------------------------------------------------------------- M14861,TRAC*01 -------------------------------------------------------------------------------- AE000662,TRAC*01 ----------------------------G--------------------------------------------------- M94081 ,TRAC*01 ----------------------------G---------------------------------------------------
X02883 ,TRAC*01 GCCCTGCTATGCTGTGTGTCTGGGCGTGTTGTATGTCCTGCTGCCGATGCCTTC X02592 ,TRAC*01 ------------------------------------------------------ M14861,TRAC*01 ------------------------------------------------------ AE000662,TRAC*01 ------------------------------------------------------ M94081 ,TRAC*01 ------------------------------------------------------
#: Nucleotide deletion or insertion

A DONOR-SPLICE, located just after the termination codon, uses a dowstream ACCEPTOR-SPLICE, placing part of the 3' non-coding sequence on a separate untranslated exon, designated as EX4.
Since EX4 is untranslated, nucleotide differences observed in EX4 are not taken into account for the description of alleles, according to IMGT allele nomenclature and sequence polymorphisms.
A mutation of the 'g' nucleotide (that follows the STOP-CODON, and corresponds to the 'n' of the 'ngt' DONOR-SPLICE,mutation g>a, leads to a splicing of EX2 to EX4, and therefore to a loss of EX3, and to an immunodeficiency in homozygous indiviuals for the mutation (Morgan N.V. et al., J. Clin. Invest; 121, 695-702 (2011) PMID: 21206088

IMGT note:
(1) Amino acid resulting from the splicing with th TRA J-REGIONs is N (codon aat) for 35 TRAJ, D (codon gat) for 12 TRAJ, Y (codon tat) for 7 TRAJ or H (codon cat) for 4 TRAJ. See Alignment of alleles: Human TRAJ (overview).


This alignement has been generated with the IMGT/AlleleAlign tool developed by Mehdi Yousfi (31/07/2001)

Created: 25/10/1999
Last updated: Friday, 27-May-2016 21:03:12 CEST
Authors: Géraldine Folch and Nathalie Bosc

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