IMGT/HLA Database--a sequence database for the human major histocompatibility complex - PubMed (original) (raw)

IMGT/HLA Database--a sequence database for the human major histocompatibility complex

J Robinson et al. Nucleic Acids Res. 2001.

Abstract

The IMGT/HLA Database (www.ebi.ac.uk/imgt/hla/) specialises in sequences of polymorphic genes of the HLA system, the human major histocompatibility complex (MHC). The HLA complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and these include the 21 highly polymorphic HLA genes, which influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The database contains sequences for all HLA alleles officially recognised by the WHO Nomenclature Committee for Factors of the HLA System and provides users with online tools and facilities for their retrieval and analysis. These include allele reports, alignment tools and detailed descriptions of the source cells. The online IMGT/HLA submission tool allows both new and confirmatory sequences to be submitted directly to the WHO Nomenclature Committee. The latest version (release 1.7.0 July 2000) contains 1220 HLA alleles derived from over 2700 component sequences from the EMBL/GenBank/DDBJ databases. The HLA database provides a model which will be extended to provide specialist databases for polymorphic MHC genes of other species.

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Figures

Figure 1

Figure 1

Simplified map of the HLA complex. The highly polymorphic (classical) HLA genes are represented in red, HLA pseudogenes in yellow and monomorphic or oligomorphic (non-classical) HLA genes are shown in green. The MICA and MICB genes which are related in structure to the HLA-A, -B and -C genes and, like HLA genes, have been shown to be highly polymorphic, are shown in pink and have been included in the database. The remaining TAP and LMP genes, turquoise and blue, respectively, encode transporter proteins and proteasome subunits, respectively. Both TAP and LMP gene products contribute to antigen presentation by HLA-A, -B and -C molecules.

Figure 2

Figure 2

Alignment formats available from the IMGT/HLA Database.The examples shown are all based on alignment A which shows seven DRB1*01 alleles. Alignment B shows these sequences with the mismatches highlighted and the sequence split into codons. In these alignments a dash (–) indicates identity to the reference sequence and an asterisk (*) denotes an unsequenced base. Alignment C shows how an alternative reference sequence can be used, here for example we have used a DRB1 consensus sequence. Alignment D represents a translation of the nucleotide sequence to produce a protein sequence alignment.

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