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How to interpret UniProt allele patterns?

Bioinformatics Asked by Guy Coder on October 1, 2021

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there are listed patterns for alleles, e.g. for 1A11_HUMAN is

The following alleles of A-11 are known:
A*11:01 (A-11E), A*11:02 (A-11K), A*11:03, A*11:04, A*11:05 and A*11:07.

I tried searching for a description of the patterns using the words allele and/or polymorphism and found nothing.

  • How are the allele patterns to be interpreted?
  • Is there a search term to be used when looking for the patterns?
  • Also, is there an official repository of the alleles?

The answer does not have to explain the specifics of the example given.


Example of explanation of other allele pattern from here

enter image description here

This explanation of the patterns doesn’t explain the part of the pattern in UniProt like (A-11E).

One Answer

These are cytotoxic T-cell HLA alleles. HLA genotyping is very common and easy to do, so Genbank is the repository.

A*11:01 has very high frequency in Aborigine populations here . You can explore the population genetics and the past, present and current population genetics distributions per population of HLA at http://www.allelefrequencies.net/

Answered by M__ on October 1, 2021

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