Table 3. Over-represented 8-mer motifs in CNEs of cluster #3 genes.

				Known TFBS
No.	Motif (and reverse-complement)	No. of instances	P-value	Sequence	TF	References
1	ATTAACCG (CGGTTAAT)	159	1.1×10−12	ATGYTAAT	Brn2	[64]
2	CTAATTAG (palindromic)	276	6.8×10−8	GCATAATTAAT	Brn3	[65]
				TAATTA	HoxB1, HoxB3	[66]
3	CATTAGCG (CGCTAATG)	98	5.2×10−4	CYYNATTAKY	HoxA5	[67]
				CATTAG	Isl-1	[68]
4	TGATTACG (CGTAATCA)	124	4.2×10−3	AATTAATCAA	Pit-1	[69]

Human-fugu CNEs of cluster #3 human transcription factor-encoding genes were compared against CNEs of non-cluster #3 transcription factor-encoding genes. Number of instances of each motif was determined by searching each motif in the human-fugu CNEs permitting at most 2 mismatches. P-values were calculated based on a chi-squared test followed by Bonferroni correction for multiple testing. Underlined portion of TFBS sequence indicates similarity with motif. TF, transcription factor; TFBS, TF binding sites.