Fig. 1

Schematic workflow. Based on conservation across Arabidopsis accessions containing SNPs (vertical red bars), positional preferences (indicated as frequency profiles), and occurrence differences of hexamers in first introns relative to other introns (horizontal bars illustrate a particular candidate hexamer), candidate hexamer motifs were identified. To test for functional relevance, correlation of gene expression among genes containing a potential motif was compared to correlations of gene expression of sets of genes containing hexamers with comparable frequency. Hexamers with the highest correlation were selected and consensus motifs were determined. To validate both hexamer and consensus motifs, natural variations among Arabidopsis thaliana accessions were utilized. For genes containing a motif of interest in their first intron and with detected naturally occurring mutations, accessions were split into the canonical/reference (containing the original motif) and the non-canonical/variant (mutated motif) allele set, and expression levels of the different alleles were compared. Figure created with BioRender.com