The HLA alleles and the allele alignments data are obtained from IMGT/HLA database (IMGT/HLA release version 3.10.0, October, 2012). Please refer the following publications for information regarding the IMGT/HLA database and the hla.allele.org database:

  • Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SGEL: The IMGT/HLA database, Nucleic Acids Research (2009), 37:D1013-7
  • Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE: IMGT/HLA - a sequence database for the human major histocompatibility complex, Tissue Antigens (2000), 55:280-287

A complete list of all of the HLA sequence features and their variant types can be found in the Supplemental Tables to Karp et al (2010) Human Molecular Genetics 19(4):707-719.

For more information on the sources of data for the MHC component in ImmPort, please see below.

Fields marked with an asterisk * are required.

 
Please Choose Query Type
General Criteria:
Species
Locus *
Allele Criteria:
Search For *  
Search Using *  
Search Option*  
Search Text   
(Comma delimited)
Results per page:


Using Allele Search  

To find allele records for a given MHC locus:

  • Choose "Allele" from the query type drop-down box.
  • Choose whether you want to return all alleles, alleles with g-code definitions or CWD alleles (see definitions below).
  • Search for alleles using allele names, IMGT accession number, G-Code grouping or transcript or protein sequence
  • Choose the "Allele Search Option" to help refine your search. Note: for a search using transcript or protein sequence the "Like" search option is a string match operator and is not blast-based.
  • Enter your search text (examples shown below). All searches are case-insensitive. Multiple inputs should be separated by a comma. Leave the "Allele Search Text" box empty to return all allele records for the selected locus.

To view alignments for a specific allele or set of alleles:

  • Choose "Alignment" from the query type drop-down box.
  • Select the type of sequence (genomic, protein or transcript) from the "Sequence Type" drop-down box and indicate the span over which the alignment should be performed.

To view sequence features and sequence feature variant types for a specific allele or set of alleles:

  • Choose "Sequence Feature" from the query type drop-down box.
  • Search for sequence features, based on functional or structural characteristics or specific amino acid positions.
  • Enter any particular Feature Name of interest. Click here for a complete listing of sequence feature names and their definitions.
  • Enter any amino acid position of interest in the "Feature Locations" box.

    Allele Search Using OptionExample Allele Search Text
    Allele NameA*02:07 or A*0207, or 02:07 or 0207or any comma-delimited combination
    IMGT Accession NumberHLA00012 or 00012
    IMGT/HLA G-Code Group CodeA*01:01:01G or 01:01:01G or A*01:01:01 or 01:01:01
    IMGT/HLA P-Code Group CodeA*01:01P or 01:01P or A*01:01 or 01:01
    Protein SequenceFASTA sequence (no spaces)
    Transcript SequenceFASTA sequence (no spaces)

--Common and Well-Documented (CWD) HLA alleles refer to those alleles that have gene frequencies of > 0.001 in any reference population or have been observed in at least three independent, unrelated individuals.
--G-codes describe groups of HLA alleles with identical sequences in the exons encoding the MHC antigen recognition site (exons 2 & 3 in class I MHC genes and exon 2 in class II MHC genes).
--CWD alleles and g-codes are described in the paper, "Common and Well-Documented HLA alleles: Report of the Ad-Hoc Committee of the American Society for Histocompatibility and Immunogenetics" [17462507].
--G-code grouping data was enhanced with ambiguity typing data obtained from Anthony Nolan, [IMGT/HLA Database].
--Population data used for generation of allele frequencies was obtained from dbMHC, [Human Anthropology].
-- HLA sequence features and their variant types are described in the paper "Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis" [19933168]. Tables containing detailed descriptions of all HLA SFVTs can be found here.

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