Cetacea
Welcome to the IPD-MHC Cetacea Leukocyte Antigen (CeLA) database, a specialist database for the Major Histocompatibility Complex genes for the infraorder Cetacea. This is intended to become the central source of information on cetacean MHC – to collate data on genes, proteins and their polymorphisms and provide a forum for their analysis and nomenclature. The database includes baleen whales and toothed whales. At present, it contains more than 100 class IIa alleles for DRA, DRB1, DQA, and DQB from twenty different cetacean species. These are complete exon2 MHC class IIa sequences as described in the reference article below. Full-length sequences for class I, DRA, DQA and DQB are sourced from genome assemblies from the Bottlenose dolphin (Tursiops truncatus) and Blue whale (Balaenoptera musculus) EMBL and NCBI. The aim is to expand the database to any cetacean species for which MHC class IIa data has been generated as well as to class I sequences.
Alleles
List all Cetacea alleles
Species
Species belonging to the Cetacea group
Align
Multi locus inter- and intra- species alignment
Nomenclature
The nomenclature guidelines for Cetacea closely follow the guidelines for other species already established in the IPD-MHC database. For the IPD-MHC, ideally, complete sequences for exon 2 for class IIa genes, and exon2 and 3 for class I genes should be submitted. However, recognizing the non-model status for cetacean species, the difficulty of obtaining samples, and while transitioning established alleles to a centralized and curated database, partial sequences will be accepted initially. Only those sequences whose genomic location has been unambiguously recognized will be assigned to a particular locus; all others will be prefixed “N” for “not assigned”. Allele names are based on amino acid sequence and are numbered for each locus and species in a single series.
Euau-DQB
15
Class II
Meno-DQB
14
Class II
Tutr-DQB
5
Class II
Tutr-DRB1
3
Class II
Tutr-DQA
3
Class II
Cehe-DQB
2
Class II
Dede-DQB
2
Class II
Stbr-DQB
2
Class II
Mede-DRA
2
Class II
Laob-DQA
2
Class II
Above are listed the most populated genes within the Cetacea group. To list all the genes within the CeLA taxonomic group, please visit the species page.
Search CeLA alleles
Group curator
Dr. Dorothea Heimeier - d.heimeier [at] auckland.ac.nz
University of Auckland, School of Biological Sciences, New Zealand
References
Heimeier, D., Garland, E. C., Eichenberger, F., Garrigue, C., Vella, A., Baker, C. S., & Carroll,E. L. (2024). A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Molecular Ecology Resources, 24, e13955. https://doi.org/10.1111/1755-0998.13955