Figure 1. Physical map of the horse MHC class II region.

Sequence assembly of eight BAC clones constituting a minimum-tiling path. Consecutively numbered junctions are indicated with grey shading and Arabic numerals. The BAC clone assembly forms two contigs, Contig 1 and 2, joined by Amplicons 1 and 2. Blue and red colours indicates two the homologous chromosomes 20 of the horse Bravo, Chromosome A and Chromosome B. An asterisk indicates the partially sequenced BAC clone. Gene content illustrates the location and orientation of all detected genes (blue) and pseudogenes (green) with transcriptional directionality indicated by arrows. Probe density describes the variation in the probe coverage over the MHC class II region. Probe mapping locations of the Axiom Equine Genotyping array are displayed as black lines. Broad Institute SNP collection probe locations are displayed as grey lines and Illumina beadchip positions are highlighted in black. GC% describes the percentage of G and C nucleotides in 1 kbp windows.