Synonymous constraint elements (SCEs) corresponding to dual-coding, selenocysteine insertion, and expression enhancer functions. (A) A large SCE (blue) fully encompasses a 66-codon sense/antisense dual-coding region in the convergent transcripts of THRA and NR1D1. The SCE is specifically localized to the overlapping exons, while upstream exons of each gene are excluded. (B) A predicted SCE in the selenoprotein-encoding gene SEPHS2 encompasses the selenocysteine insertion site (red) and a predicted RNA hairpin structure (minimum free energy fold rendered by VARNA) (Darty et al. 2009) immediately downstream from the selenocysteine codon. Inferred structure is similar to a hairpin known to stimulate selenocysteine recoding in SEPN1 (Howard et al. 2005). (C) Two SCEs are found within the HOXA2 ORF, each corresponding to a different enhancer element regulating expression of the mouse ortholog in distinct segments of the developing hindbrain. The 5′ element encodes a HOX-PBX responsive element and drives expression in rhombomere 4 (Lampe et al. 2008), and the 3′ element encodes SOX2 binding sites and drives expression in rhombomere 2 (Tümpel et al. 2008). The 3′ element includes several RTE and ACAAT motif instances that were investigated by site-directed mutagenesis in the previous study (red), as well as two additional upstream instances (green). SCEs are also found within most other HOX genes.
