The positions of the Six1 exons are shown at the bottom in blue. The lightest shade is intron, intermediate shade is coding, and darker blue represents 5′ and 3′ UTR. The cranial mesenchyme, top panel, shows strong expression with many RNA-seq reads, marked by small tan rectangles. The lines indicate positions of introns, where single cDNA RNA-seq reads align to the two flanking exons. Note the many reads from the 5′ region of Six1 in the top panel, coincident with high expression of the Six1 one gene itself. In the dorsal neural fold, bottom panel, there is very low expression of both the Six1 gene and the 5′ flanking region.