Salmonids

Welcome to the IPD-MHC FISH database, a specialist database for the Major Histocompatibility genes of salmonid fish. The database includes at present two salmonid species: Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Atlantic salmon and rainbow trout possess a single classical MHC class I locus, UBA, and a single classical MHC class II molecule encoded by closely linked DAA (IIA) and DAB (IIB) loci. Included in the database are full-length and/or nearly complete peptide binding domain-coding sequences from published studies and from the EMBL and NCBI databases.

For those readers who would like to know more about MHC sequences in salmonids, please see the Introduction MHC page.

Alleles

List all Salmonids alleles

Species

Species belonging to the Salmonids group

Align

Multi locus inter- and intra- species alignment

Nomenclature

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

  • Each allele name has a unique number corresponding to up to four sets of digits separated by colons.
  • Double-digit 1 plus 2 (*01 or *02, etc.) indicates a group of divergent 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., 01:01, 01:02, etc.)(< 4 amino acids difference between class I alleles, < 3 amino acids difference between class II alleles)
  • 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., 01:01:01, 01:01:02, 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".

Onmy-UBA

48

Class I

Sasa-UBA

48

Class I

Sasa-DAB

42

Class II

Sasa-DAA

22

Class II

Onmy-DAB

22

Class II

Onmy-DAA

3

Class II

Above are listed the most populated genes within the Salmonids group. To list all the genes within the FISH taxonomic group, please visit the species page.

Search FISH alleles

Group curator

Dr. Unni Grimholt - Unni.Grimholt [at] vetinst.no

Norwegian Veterinary Institute, Genetic, Norway

References

This database was initiated and maintained from 2006 to 2007 by Prof. René J.M. Stet, who sadly passed away in the middle of a career highlighted by many essential contributions to the field of fish MHC research.

  • Parham P René Stet: 1954-2007 Immunogenetics (2008) 60:73-75
  • Dixon B René Stet's impact on the study of teleost major histocompatibility genes: evolution from loci to populations Immunogenetics (2008) 60:77-82

When René J.M. Sted died, this database was continued by Dr. Hans (J.M.) Dijkstra, assisted by Dr. Unni Grimholt and Dr. John D. Handsen. Sequences are now curated by Dr. Unni Grimholt (Norwegian Veterinary Institute, Oslo, Norway. Email: unni.grimholt@vetinst.no)

Please cite:

  • Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, De Groot NG, Flicek P, Bontrop RE, Hammond JA and Marsh SGE IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. Nucleic Acids Res. (2017), 45: D860–D864