Using a comparative genomics approach to reconstruct the fate of genomic 
regulatory blocks (GRBs) and identify exonic remnants that have survived the 
disappearance of their host genes after whole-genome duplication (WGD) in 
teleosts, we discover a set of 38 candidate cis-regulatory coding exons (RCEs) 
with predicted target genes. These elements demonstrate evolutionary separation 
of overlapping protein-coding and regulatory information after WGD in teleosts. 
We present evidence that the corresponding mammalian exons are still under both 
coding and non-coding selection pressure, are more conserved than other protein 
coding exons in the host gene and several control sets, and share key 
characteristics with highly conserved non-coding elements in the same regions. 
Their dual function is corroborated by existing experimental data. Additionally, 
we show examples of human exon remnants stemming from the vertebrate 2R WGD. Our 
findings suggest that long-range cis-regulatory inputs for developmental genes 
are not limited to non-coding regions, but can also overlap the coding sequence 
of unrelated genes. Thus, exonic regulatory elements in GRBs might be 
functionally equivalent to those in non-coding regions, calling for a 
re-evaluation of the sequence space in which to look for long-range regulatory 
elements and experimentally test their activity.