Fig. 1
UCSC Genome Browser view of the mouse 15qD1 gene desert (upper) and orthologous human 8q24 cancer-associated gene desert (lower) proximal to the proto-oncogene, MYC, and distal to the gene, FAM84b. The mouse-human conserved protein-coding genes in the region are Myc and Fam84b indicated in purple shading. The conserved long non-coding RNA (lncRNA) gene, Pvt1, is also indicated in purple shading. The mouse A1bg gene (in light yellow shading) is not conserved in human and it is not expressed in mouse mammary gland. The human non-coding transcripts located in the gene desert (i.e. PCAT1, PCAT2, PRNCR1, POU5F1B, CCAT1, CCAT2, CASC8, CASC11, CASC19, CASC21) do not have mouse orthologs, although non-coding transcripts are produced from the mouse gene desert as well (i.e. D030024E09Rik, Gm29904, Gm38563, 4930402D18Rik). The breast cancer-associated variants rs13281615, rs1562430, and rs35961416, and their respective correlated variants (level of r2 correlation in CEU population shown on y-axis) are indicated on separate tracks. The Multi-Z alignment tracks indicate good conservation from human to mouse, especially in the areas where the breast cancer variants with highest correlation level are located. The ORegAnno track (mouse) and DNAseI Hypersensitivity track (human) indicate potential gene regulatory elements. The red bar represents the mouse megadeletion (MD) interval (430-Kb). The deleted interval encompasses the region orthologous to the breast cancer-associated and correlated variants. The deletion interval recently generated in an unrelated study by Dave et al. is indicated in dark yellow [23]