Organization of the leukocyte receptor complex on human chromosome 19q13.4. Two contigs were deduced from PACs positive with combinations of individual probes. The complete sequences of PACs 1060P11² and 52N12¹ are displayed in Figs. 2 and 4, respectively. A sequence of a section of the KIRs from a haplotype similar to that of 72N6¹ is available (GenBank database accession no. AC011501). The KIR gene family is flanked by the ILT cluster I and the FcαR gene. The numbers of KIR genes differ depending on the haplotype. The ILT genes are grouped in two clusters separated by the LAIR genes. A link between the two clusters remains to be established. Marker 204 is based on a PCR product designed for other sequences in the database. Although all PAC sizes are to scale, distances between genes outside the sequenced region are approximate. At the telomeric end, the gene designated X is not related structurally to the Ig-like receptors. 52N12¹ and 72N6¹ represent one haplotype, and the contig containing 167B21² is part of the second haplotype. This was based on sequence polymorphism in the PCR-amplified ILT3 gene and other differences. Arrows point 5′ to 3′.

(A) Feature map of the complete sequence of the KIR region on PAC 1060P11². The exons of the KIR genes are shown corresponding to cDNAs or by homology with other genes (KIR3DL3, KIRX). Arrows point 5′ to 3′. The positions of Alu, LINE, and LTRs are indicated on the lines below the genes. KR indicates G+C-rich minisatellites specific to KIR genes. (B) Dot matrix analysis of the sequence from PAC 1060P11². The plot shows the 10 KIR genes on the PAC on both x and y axes. Regions of similarity are identified as a concentration of dots forming diagonal lines (22). The G+C-rich minisatellites can be visualized as boxes, missing in KIR2DL4. Insertions/deletions are visible in KIR2DL4 and KIR2DS5.

(A) Differences in the organization of the KIR region in two different haplotypes. On the top line is the plot of the KIR region from 1060P11² (Fig. 2A). Partial sequence was obtained from PACs 72N6¹, 78E4¹, 1015E9¹, and 1015 M9¹ for the other haplotype (Fig. 1) by using PCR as well as comparison with other data (see Fig. 1). The gene distances are not to scale and have been exaggerated to display contiguity, suggested by sequence comparisons. Thus, 2DL2 is shown as a composite of two genes on the second haplotype, namely 2DL3 and 2DL1. Overall, the genes are so similar that the precise lineup of the alleles remains uncertain, but 3DS1 and 3DL1 are shown as alleles, as supported by other data (see below and ref. 16). (B) Framework genes and variable bubbles in the KIR region. Comparison of the gene organization data in Fig. 2A, from the two haplotypes, with other data (16) is consistent with invariant framework loci, flanking regions where the gene number shows marked flexibility, indicated as open boxes flanked by square boxes. A similar model has been proposed to explain (mostly interspecies) gene expansion/contraction in the MHC, proposing independent expansion of class I genes within a framework of ancestral loci (48).

(A) Organization of ILT cluster I. Sequence of the six ILT genes clustered within 150 kb centromeric of the KIR from PAC 52N12¹. All genes are in the same 5′ to 3′ orientation from centromere to telomere and, with exception of the ILT1 gene, are less than 6 kb in size. Fragments of ILT and LAIR exons were found throughout the entire sequence (indicated as open blocks). The exon/intron organization of the two inhibitory ILT genes, ILT2 and ILT3, is conserved, although two exons accounting for two additional Ig domains are present in the ILT2 gene. Some variation was observed between the genes encoding for putative activating ILTs: ILT1 contains an 11-kb intron between the fourth Ig domain and the stalk exon, and an extra stalk exon was found in the LIR6 gene that is not in any other activating member. In four genes, we predicted an extra 5′ untranslated region exon as seen in some LIR6 and ILT2 transcripts. (B) Dot matrix analysis of the sequence from PAC 52N12¹. The plot shows the region encompassing the five ILT genes and one LIR locus on both axes (see Fig. 4A for details). In contrast to the KIR loci (Fig. 2A), the sequences of the intergenic regions are not conserved.

(A) Haplotypic variation for presence of ILT6 in ILT cluster II. The centromeric cluster of ILT genes (Fig. 1) contained six genes in most haplotypes. On the haplotype shown (Top), the ILT6 gene is missing. (B) PCR analysis for the presence of ILT6. The genotypes of 25 individuals were analyzed by PCR by using ILT6- and ILT4-specific primers. The two samples that were negative for ILT6 are indicated by arrows.