Alignment of alleles: Torafugu (Takifugu rubripes) TRAC

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).

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

Exon names are shown between parentheses on the first line.
The Cysteines involved in the TR EX1 intrachain disulfide bridge are shown with a larger letter C in purple.
Other Cysteines (including those involved in the interchain disulfide bridge) are shown with a larger letter C in black.
STOP-CODON is indicated by an asterisk.

N (Asn, asparagine) of potential N-glycosylation sites (NXS/T, where X is different from P), (N-linked glycosylation) is shown is green (site is underlined in CHS and in pages edited before 14/10/2009).

                                                                                                               

                                                                        1.1   1   2   3   4   5   6   7   8   9  10  11
                                                                         G   D   Q   Y   Q   P   S   F   Y   K   L   K     
  AF110525,TRAC*01 (EX1)                                              (G)GG GAC CAG TAC CAA CCG TCC TTT TAC AAG CTG AAA 
                                                                                                               
  AF269222,TRAC*02 (cDNA)                                             (-)-- --- --- --- --- --- --- --- --- --- --- --- 

                                                       ___AB_______                                            ________
                                                       15.1    15.3                                                    
                                         12  13  14  15    15.2      16  17  18  19  20  21  22  23  24  25  26  27  28
                                                                         H   G   N   T   S   A   C   L   A   T   G   F 
  AF110525,TRAC*01 (EX1)                ... ... ... ... ... ... ... ... CAT GGA AAC ACC AGC GCA TGT CTG GCC ACA GGT TTC
                                                                                                               
  AF269222,TRAC*02 (cDNA)               ... ... ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- --- --- ---

                                       _________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    
                                         S   R           F   H   Q   L   Q   N   N   T   L   F   S                     
  AF110525,TRAC*01 (EX1)                AGC AGA ... ... TTC CAC CAA CTT CAG AAC AAC ACA TTG TTC AGC ... ... ... ... ...
                                                                                     A                                 
  AF269222,TRAC*02 (cDNA)               --- --- ... ... --- --- --- --- --- --- --- G-- --- --- --- ... ... ... ... ...

                                       ________                                _________________________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
                                                 Q   S   K   A   V   L   I   S   Q   D   S
  AF110525,TRAC*01 (EX1)                ... ... CAA TCT AAA GCA GTC CTG ATC TCT CAG GAC TCG ... ... ... ... ... ... ...
                                                         E                                                             
  AF269222,TRAC*02 (cDNA)               ... ... --- --- G-- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ...

                                       ________________                                                _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
                                             L   F   N   Q   V   A   F   M   D   Q   D   A                                    
  AF110525,TRAC*01 (EX1)                ... CTC TTT AAC CAG GTG GCC TTC ATG GAC CAG GAC GCG ... ... ... ... ... ... ...
                                                                                                               
  AF269222,TRAC*02 (cDNA)               ... --- --- --- --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ...

                                                                ____FG____
                                                                 
                                         99 100 101 102 103 104 105 106 
                                         D   G   E   T   S   C   P   E  
  AF110525,TRAC*01 (EX1)                GAT GGG GAA ACC AGC TGT CCT GAA G

 
  AF269222,TRAC*02 (cDNA)               --- --- --- --- --- --- --- --- -




                                         1   2   3   4   5   6   7   8   9  10  11  12  13  14  15                               
                                         D   E   N   E   G   A   V   R   C   D   D   A   L   Q   P  
  AF110525,TRAC*01 (EX2)                 AT GAG AAT GAA GGA GCT GTT CGC TGC GAC GAT GCT CTG CAG CCC G
                                                                                            
  AF269222,TRAC*02 (cDNA)                -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- -



                                         1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20                               
                                         D   P   L   V   N   L   V   S   L   M   V   T   G   L   R   V   L   L   L   K 
  AF110525,TRAC*01 (EX3)                 AC CCG CTG GTG AAC TTG GTG TCT CTG ATG GTC ACA GGA CTT CGT GTG CTC CTC CTG AAG
                                                                                                               
  AF269222,TRAC*02 (cDNA)                -- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---

                                         21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36                               
                                         T   M   I   F   N   I   L   M   T   L   R   L   R   I   S   Q  
  AF110525,TRAC*01 (EX3)                ACA ATG ATC TTC AAT ATC CTG ATG ACT CTT CGT CTG CGT ATC AGT CAG T
                                                     L                                                  
  AF269222,TRAC*02 (cDNA)               --- --- --- --A --- --- --- --- --- --- --- --- --- --- --- --- -




  AF110525,TRAC*01 (Untranslated EX4    CATCAGCCGAACCTCAGAGCTGGGTCTGACGGTCACACGTGATGTGTATAATTCCTTCTCTTACTGCTGATGTAAATAT
                          and 3'UTR)
  AF269222,TRAC*02 (cDNA)               -------------------------------------------------------------------------------


  AF110525,TRAC*01 (EX4)                TTCAGTTGTGATGGTAAAATTTGAGCTTTATTCAGTAAAAATGTGATGAAATAAA                            160
                                                                                                               
  AF269222,TRAC*02 (cDNA)               -------------------------------------------------------

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.

Created: 30/06/2003
Author: Nathalie Bosc