Comparative genomics using Fugu reveals insights into regulatory subfunctionalization

Table 3 Co-ortholog CNEs that are also conserved in the vicinity of trans-dev paralogs in the human genome

Gene region	Co-ortholog 1	Co-ortholog 2	Gene paralog in the vicinity of the dCNE(s)
BCL11A	CRCNE00002445	CRCNE00004614	BCLL1B
	CRCNE00002557	-
	CRCNE00002548	CRCNE00004648
	CRCNE00002544	CRCNE0004643
		CRCNE0004644
	CRCNE00002540	-
EBF1	CRCNE00010771	-	EFB3
	-	CRCNE00010818
	CRCNE00000027	CRCNE00010823
	CRCNE00010778	CRCNE00010827
	CRCNE00010787	-
EBF1	CRCNE00010772	CRCNE00010820	EBF1/2/3/4
PAX2	CRCNE00000064	CRCNE00000133	PAX8
PAX2	CRCNE00000071	CRCNE00000147	PAX5
	CRCNE00000090	CRCNE00000165
	CRCNE00000092	CRCNE00000167
	CRCNE00000099	CRCNE00000174
SOX1	-	CRCNE00001926	SOX2
ZNF503	CRCNE00010112	CRCNE00004977	ZNF703
	CRCNE00010147	CRCNE00004994
	CRCNE00010126	CRCNE00005024
	CRCNE00010167	-
	CRCNE00010170	-
	CRCNE00010187	-
	CRCNE00010180	-
	CRCNE00010176	CRCNE00005013
		CRCNE00005015
	CRCNE00010165	CRCNE00005011
	CRCNE00010161	CRCNE00005008
	CRCNE00010046	CRCNE00004906
	CRCNE00010156	CRCNE00005003
	CRCNE00010120	CRCNE00004986

CNEs in each co-ortholog are referred to by their CONDOR database identifiers [53]. Each CNE was considered duplicated if the human sequence they are conserved to shows significant hit to a sequence elsewhere in the genome through BLAST. Any gene in the vicinity (<1.5 Mb away) of the BLAST hit that is paralogous to genes within a window of the same size around the query CNE is shown in the final column.

ISSN: 1474-760X