Alignment References
The IPD-IMGT/HLA database uses specific reference sequences in the generation of our alignments. These references are historically chosen and unless under exceptional circumstances - such as the deletion of an allele - are not subject to change. Using one constant reference across different versions of the database allows for continuity of alignments between releases. THe following table lists the reference sequences as of Release 3.62 (2025-10)
| Locus | CDS Reference | CDS Accession | Genomic Reference | Genomic Accession |
|---|---|---|---|---|
| A | A*01:01:01:01 | HLA00001 | A*01:01:01:01 | HLA00001 |
| B | B*07:02:01:01 | HLA00132 | B*07:02:01:01 | HLA00132 |
| C | C*01:02:01:01 | HLA00401 | C*01:02:01:01 | HLA00401 |
| E | E*01:01:01:01 | HLA00934 | E*01:01:01:01 | HLA00934 |
| F | F*01:01:01:01 | HLA01096 | F*01:01:01:01 | HLA01096 |
| G | G*01:01:01:01 | HLA00939 | G*01:01:01:01 | HLA00939 |
| H | H*01:01:01:01 | HLA02546 | H*01:01:01:01 | HLA02546 |
| J | J*01:01:01:01 | HLA02626 | J*01:01:01:01 | HLA02626 |
| K | K*01:01:01:01 | HLA02654 | K*01:01:01:01 | HLA02654 |
| L | L*01:01:01:01 | HLA02655 | L*01:01:01:01 | HLA02655 |
| N | N*01:01:01:01 | HLA18596 | N*01:01:01:01 | HLA18596 |
| P | P*01:01:01:01 | HLA02742 | P*01:01:01:01 | HLA02742 |
| S | S*01:01:01:01 | HLA18607 | S*01:01:01:01 | HLA18607 |
| T | T*01:01:01:01 | HLA16376 | T*01:01:01:01 | HLA16376 |
| U | U*01:01:01:01 | HLA18591 | U*01:01:01:01 | HLA18591 |
| V | V*01:01:01:01 | HLA02801 | V*01:01:01:01 | HLA02801 |
| W | W*01:01:01:01 | HLA16364 | W*01:01:01:01 | HLA16364 |
| Y | Y*01:01 | HLA13320 | Y*01:01 | HLA13320 |
| DRA | DRA*01:01:01:01 | HLA00662 | DRA*01:01:01:01 | HLA00662 |
| DRB1 | DRB1*01:01:01:01 | HLA00664 | DRB1*01:01:01:01 | HLA00664 |
| DRB2 | DRB1*01:01:01:01 | HLA00664 | ||
| DRB3 | DRB1*01:01:01:01 | HLA00664 | DRB3*01:01:02:01 | HLA00887 |
| DRB4 | DRB1*01:01:01:01 | HLA00664 | DRB4*01:01:01:01 | HLA00905 |
| DRB5 | DRB1*01:01:01:01 | HLA00664 | DRB5*01:01:01:01 | HLA00915 |
| DRB6 | DRB1*01:01:01:01 | HLA00664 | ||
| DRB7 | DRB1*01:01:01:01 | HLA00664 | ||
| DRB8 | DRB1*01:01:01:01 | HLA00664 | ||
| DRB9 | DRB1*01:01:01:01 | HLA00664 | ||
| DQA1 | DQA1*01:01:01:01 | HLA00601 | DQA1*01:01:01:01 | HLA00601 |
| DQA2 | DQA2*01:01:01:01 | DHLA26079 | DQA2*01:01:01:01 | HLA26079 |
| DQB1 | DQB1*05:01:01:01 | HLA00638 | DQB1*05:01:01:01 | HLA00638 |
| DPA1 | DPA1*01:03:01:01 | HLA00499 | DPA1*01:03:01:01 | HLA00499 |
| DPA2 | DPA2*01:01:01:01 | HLA16384 | DPA2*01:01:01:01 | HLA16384 |
| DPB1 | DPB1*01:01:01:01 | HLA00514 | DPB1*01:01:01:01 | HLA00514 |
| DPB2 | DPB2*01:01:01 | HLA14837 | DPB2*01:01:01 | HLA14837 |
| DMA | DMA*01:01:01:01 | HLA00485 | DMA*01:01:01:01 | HLA00485 |
| DMB | DMB*01:01:01:01 | HLA00489 | DMB*01:01:01:01 | HLA00489 |
| DOA | DOA*01:01:01 | HLA00494 | DOA*01:01:01 | HLA00494 |
| DOB | DOB*01:01:01:01 | HLA01098 | DOB*01:01:01:01 | HLA01098 |
| HFE | HFE*001:01:01 | HLA14067 | HFE*001:01:01 | HLA14067 |
| MICA | MICA*001 | HLA01013 | MICA*001 | HLA01013 |
| MICB | MICB*001 | HLA02033 | MICB*002:01:01 | HLA02059 |
| TAP1 | TAP1*01:01:01:01 | HLA00953 | TAP1*01:01:01:01 | HLA00953 |
| TAP2 | TAP2*01:01:02 | HLA06625 | TAP2*01:01:02 | HLA06625 |