KIR Alignment Tool

Where discrepancies have arisen between reported sequences and those stored in the database, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and the Nomenclature Committee would welcome any evidence that helps to maintain the accuracy of these sequence alignments.

STEP 1 - Select the gene and feature to align

STEP 2 - Select sequences and reference




STEP 3 - Select how you view the alignment




STEP 4 - Proceed with the alignment


Help with the Sequence Alignments

  • The KIR genes do not all express the same number of exons, some genes like 2DL1, 2DL2, 2DL3 and the 2DS genes have a pseudoexon where exon 3 would normally be found. To maintain the alignments, in these genes the third expressed exon is refered to as exon 4, and subsequent exons numbered sequentially. Other genes like 2DL4 and 2DL5 have a deletion of exon 4, and 3DL3 has a deletion of exon 6, in these cases the region aorund this deletion will be referred to as intron 3/4 and intron 5/6 respectively. The alignment tool uses the exon and intron numbering detailed in Figure 2 of the Introduction.
  • The "Nucleotide - CDS plus pseudoexon" option incorporates the pseudoexon sequence found in some genes (2DL1, 2DL2, 2DL3, 2DS1, 2DS2, 2DS3, 2DS4 and 2DS5) into the CDS alignment.
  • A default reference sequence for all genes is automatically provided. This can be changed by entering a new allele name in the box provided. If the allele code entered is incorrect or unavailable a default reference sequence will be used. If you wish to view a consensus sequence of the alleles selected enter "CONSENSUS" as the reference sequence in the box provided.
  • To view an alignment of specific sequences rather than all availalbe alleles enter the common nomenclature or list the allele names separated by a comma.
  • Where discrepancies have arisen between reported sequences and those stored in the database, the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and the Nomenclature Committee would welcome any evidence that helps to maintain the accuracy of these sequence alignments.
  • You may need to widen your browser to view the output. If you need to alter the size of the text use 'Ctrl' and '+' or '-' on a PC or 'Apple' and '+' or '-' on Mac. These keys may vary depending on your choice or browser.

Further more detailed help can be found in the help file which details both the input options and how the alignments are displayed.

IPD-KIR