In mammals the THRA gene is alternatively spliced and encodes two proteins. TRα1 is the α‐thyroid hormone receptor, which is widely expressed in all vertebrates. TRα2 is a non‐hormone‐binding variant, present only in eutherian mammals. Coding sequences unique to TRα2 share an antisense overlap with those of Rev‐erbα, a nuclear receptor and core component of the mammalian circadian clock. Intronic and exonic splicing enhancers for TRα2 have evolved in the context of sequences required expression of Rev‐erbα mRNA. Of particular interest is a GC‐rich region (G30) within the C‐terminal sequence of TRα2 mRNA and antisense to the 3'UTR of Rev‐erbα. Closely spaced deletions and substitutions within G30 have dramatically different effects on TRα2 splicing depending on their precise structure and position. For example, deletion of 12 nucleotides can lead to >;95% inhibition or >;2.5‐fold enhancement of TRα2 splicing. Substitutions of 5–8 bases within G30 also display a range of effects. Our results suggest that G30 is a highly structured sequence, possibly a G‐quadruplex, and part of a larger complex splicing regulatory element that exerts both positive and negative effects on TRα2 expression.