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IPD-MHC Database

Fish Nomenclature

Nomenclature Tables

Atlantic salmon and rainbow trout possess a single classical MHC class I locus, UBA, and a single classical MHC class II locus consisting of closely linked DAA (IIA) and DAB (IIB). Included in the database are full-length and nearly complete peptide binding domain-coding sequences from published studies and from the EMBL and NCBI databases.

The number of sequences presently described in this database inlcude:

  1. Atlantic salmon UBA: 43 amino acid sequences deduced from 43 nucleotide sequences
  2. Rainbow trout UBA: 44 amino acid sequences deduced from 47 nucleotide sequences
  3. Atlantic salmon DAA: 20 amino acid sequence deduced from 21 nucleotide sequences
  4. Rainbow trout DAA: 3 amino acid sequences deduced from 3 nucleotide sequences
  5. Atlantic salmon DAB: 42 amino acid sequence deduced from 42 nucleotide sequences
  6. Rainbow trout DAB: 19 amino acid sequences deduced from 22 nucleotide sequences

In an attempt to be consistent, where possible the following rules were applied:

  • double-digit 1 plus 2 (01 or 02, etc.) indicates a group of similar sequences (< 4 amino acids difference between class I alleles, < 3 amino acids difference between class II alleles)
  • double-digit 3 plus 4 is used for numbering within groups of similar sequences (e.g., 0101, 0102, etc.)
  • when the amino acid sequences are identical but the nucleotide sequences are different (e.g., SNPs equating to synonymous substitutions), this is indicated by the addition of a third double-digit number (e.g.,  010101, 010102, etc.)

For consistency, many of the sequences have been renamed since their initial publication. Original names other than the current IPD database names are listed here as “Local names”. In April 2011 a number of changes were made to the allele name, the previous IPD names can be found under "Previous IPD name".

 

Atlantic salmon

Rainbow trout

Further Information

For information regarding the website and technical issues please contact IPD Support.

 


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