IPD-MHC

Nomenclature of Capra genes

Capra (CLA) MHC nomenclature follows the rules proposed by the MHC Nomenclature Committee. Sequence derived from domestic, feral and wild goats Capra hircus use the four-letter abbreviation Cahi.

Class I

As assignment of individual class I sequences to a specific class I locus is not yet possible, class I alleles will be prefixed ‘N’ to indicate ‘not assigned’ and numbered in a single series. Class I allele names are based on amino acid sequence. The first set of digits indicate the allele ‘group’, the second set separated from the first by a colon, indicate coding change, the next set indicate non-coding change, and the last set indicate promoter/intron change. While full length sequences are preferred, names will only be given to sequences that include all of exons two and three. The guidelines regarding assignment to an allele ‘group’ are that sequences within a group should have a maximum of 4 amino acid changes within the alpha 1 and 2 domains, plus up to 4 amino acid changes in any other part of the coding sequence.

Class II

DRB1, DQA and DQB alleles will each be numbered in single allelic series until grouping to an individual locus is possible. Allele names are based on amino acid sequence with the first set of digits indicating the major allelic type, the next set indicating coding change, and the next indicating silent substitutions. Each set is separated by a colon. Class II alleles of a single major allelic type should differ by no more than 4 amino acids in the first domain.

Conditions for inclusion of new CLA alleles

Guidelines for acceptance of new alleles are as follows:

1. Full length sequences are always preferable.
2. For class I genes complete exons 2 and 3 are required.
3. For class II genes we encourage submission of full length sequences for all class II loci with the exception of the principally transcribed and highly polymorphic DRB1 locus. For this locus the entire exon 2 must be included although primers which overlap the intron exon boundaries will be acceptable
4. To start a new locus a full length transcript includinge start and stop codons is required as the reference sequence
5. Sequencing should have been performed on both strands of the template DNA.
6. When a sequence is based on clones derived from PCR amplification, a minimum of three clones must have been sequenced.
7. When a sequence is based on clones derived from PCR amplification, sequences from 2 independent PCR reactions are required.
8. If a novel sequence is derived from direct sequencing of PCR products, material derived from at least two separate PCR reactions should have been sequenced.
9. Ensure that predicted amino acid sequences make sense with particular attention to unique/unusual amino acid substitutions. If in doubt sequence additional clones derived from a different PCR amplification.
10. An accession number in a nucleotide sequence database has to have been obtained.
11. DNA, or cell lines should be available for future reference and the curators retain the right to request a DNA sample for validation.

Submission of new CLA sequences

To receive official names, sequences of new CLA genes or alleles should be submitted to the IPD-MHC database. All sequence information will remain confidential until published on sequence databases.