Top 25 candidate inner ear COUP-TFI targets.

Ranking criteria (leftmost column) integrate microarray data and number of conserved COUP-TF HMM hits, as well as the degree of evoluationary conservation. P = promoter (5000bp); 5U = 5′UTR; FI = first intron of all transcripts associated with the gene. MC = Most conserved site; >0.7 = site with a conservation score greater than 0.7; >0.3 = site with a conservation score greater than 0.3. *Microarray ranking range from 1–175, higher rank numerical value with lower genotype p-value or greater fold-change. **Corresponds to a late transcription start site. ***Sites distributed in the first intron of different transcripts, or in the first intron of a particular splice variant.