Alignment of alleles: Atlantic cod (Gadus morhua) IGHV3S9

When several alleles are shown, the nucleotide mutations and amino acid changes for a given codon are indicated in red letters. These polymorphic mutations are reported in Tables of alleles.
Dashes indicate identical nucleotides. Dots indicate gaps according to the IMGT unique numbering. Blanks indicate partial sequences (blanks at the 5' and/or 3' end).

Germline genomic sequences are needed to confirm if the nucleotide substitutions result from somatic mutations or correspond to allelic polymorphisms.

                                  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20
                                 C   E   Q   L   T   Q   P   E   S       L   T   V   R   P   G   Q   P   L   T
  AJ274750,IGHV3S9*01, 12-19    TGT GAA CAG CTT ACT CAG CCA GAG TCT ... CTG ACT GTC CGA CCT GGT CAA CCT CTG ACC

  AJ274719,IGHV3S9*02, 12-11    --- --- --- --- --- --- --- --- --- ... --- --- --- --- --- --- --- --- --- ---

  AJ274731,IGHV3S9*03, 09-29    --- --- --- --- --- --- --- --- --- ... --- --- --- --- --- --- --- --- --- ---

  AJ279371,IGHV3S9*04, 33       --- --- --- --- --- --- --- --- --- ... --- --- --- --- --- --- --- --- --- ---

                                                        ___________________CDR1-IMGT____________________
                                 21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39  40
                                 I   R   C   Q   V   S   Y   S   V   S   S   Y   A                       T   A
  AJ274750,IGHV3S9*01, 12-19    ATC CGC TGT CAG GTC TCT TAT TCT GTT AGT AGC TAC GCG ... ... ... ... ... ACA GCT
                                                                                 L  
  AJ274719,IGHV3S9*02, 12-11    --- --- --- --- --- --- --- --- --- --- --- --- TT- ... ... ... ... ... --- ---
                                                                                 L  
  AJ274731,IGHV3S9*03, 09-29    --- --- --- --- --- --- --- --- --- --- --- --- TT- ... ... ... ... ... --- ---
                                                                                 L  
  AJ279371,IGHV3S9*04, 33       --- --- --- --- --- --- --- --- --- --- --- --- TT- ... ... ... ... ... --- ---

                                                                                            _______________CDR2-
                                 41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60 
                                 W   I   R   Q   P   D   G   K   G   L   E   W   I   G   W   I   Y   T   S   D
  AJ274750,IGHV3S9*01, 12-19    TGG ATC AGA CAA CCT GAT GGA AAA GGA CTG GAA TGG ATT GGA TGG ATT TAT ACC AGT GAC
                                                                                                         A  
  AJ274719,IGHV3S9*02, 12-11    --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GCG ---
                                                                                                         A  
  AJ274731,IGHV3S9*03, 09-29    --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GCG ---
                                                                                                         A  
  AJ279371,IGHV3S9*04, 33       --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GCG ---

                                IMGT________________
                                 61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79  80
                                 K                   K   V   K   D   S   F   N       S   K   F   S   L   S   L
  AJ274750,IGHV3S9*01, 12-19    AAA ... ... ... ... AAA GTG AAA GAC TCC TTT AAT ... AGT AAA TTC AGT CTT TCC CTT
                                                                         L   S  
  AJ274719,IGHV3S9*02, 12-11    --- ... ... ... ... --- --- --- --- --- C-- -G- ... --- --- --- --- --- --- ---
                                                                         L   S  
  AJ274731,IGHV3S9*03, 09-29    --- ... ... ... ... --- --- --- --- --- C-- -G- ... --- --- --- --- --- --- ---
                                                                         L   S  
  AJ279371,IGHV3S9*04, 33       --- ... ... ... ... --- --- --- --- --- C-- -G- ... --- --- --- --- --- --- ---


                                 81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 100
                                 D   E   A   S   K   T   I   T   L   Q   G   Q   N   M   Q   P   G   D   S   A
  AJ274750,IGHV3S9*01, 12-19    GAC GAG GCC AGT AAA ACA ATA ACT TTG CAA GGG CAA AAC ATG CAG CCT GGA GAC TCA GCT
                                                         G  
  AJ274719,IGHV3S9*02, 12-11    --- --- --- --- --- --- GGC --- --- --- --- --- --- --- --- --- --- --- --T ---
                                                         V  
  AJ274731,IGHV3S9*03, 09-29    --- --- --- --- --- --- G-C --- --- --- --- --- --- --- --- --- --- --- --T ---
                                                         V  
  AJ279371,IGHV3S9*04, 33       --- --- --- --- --- --- G-C --- --- --- --- --- --- --- --- --- --- --- --- ---

                                                CDR3-IMGT
                                101 102 103 104 105 106 
                                 V   Y   Y   C   A   E
  AJ274750,IGHV3S9*01, 12-19    GTG TAT TAC TGT GCC GAA    #c
                                                     G
  AJ274719,IGHV3S9*02, 12-11    --- --- --- --- --- -GG    #c
                                                     R
  AJ274731,IGHV3S9*03, 09-29    --- --- --- --- --- AG-    #c
                                                     R
  AJ279371,IGHV3S9*04, 33       --- --- --- --- --- AG-    #c
#c: rearranged cDNA

This alignment of allele is automatically generated by Mehdi Yousfi alignment of allele tool.

Created: 21/01/2002
Author: Nathalie Bosc