Table 1.

The candidate set of RCE host genes

ID	Target gene (Tg)	RCE host gene (Bg)	Number of total exons	Number of remnant exons	Number of class I(II) remnants	Number of HCNEs within host gene
1	PAX6	ELP4	12	2	2 (0)	36
2	WT1	EIF3M	11	2	2 (0)	2
3	ZIC2	PCCA	25	3	1 (2)	33
4	EYA1	KCNB2	2	1	1 (0)	0
5	PROX1	RPS6KC1	15	3	3 (0)	9
6	TWIST1	HDAC9	25	2a	1 (1)	2
				3b	3 (0)	7
7	FOXP2	PPP1R3A	4	1	1 (0)	0
8	LHX1	ACACA	56	2	1 (1)	13
9	NR2F1	O94914_HUMAN	9	3	1 (2)	1
10	IRX3	RPGRIP1L	26	1	1 (0)	8
11	GSX2	CHIC2	6	2c	0 (2)	3
12	TSHZ1	ZNF407	7	1	1 (0)	36
13	EVX2	MTX2	10	2	2 (0)	4
14	ZNF536	C19orf2	11	1	1 (0)	1
15	FIGN	KCNH7	17	1	1 (0)	0
16	LBXCOR1	MAP2K5	22	3	1 (2)	15
17	SMAD3	IQCH	21	1	1 (0)	2
18	SP3	OLA1	10	2	2 (0)	12
19	DLX2	SLC25A12	18	2	2 (0)	0

Summary table for 19 RCE host genes (Bg) and the corresponding target genes (Tg). For each RCE host gene, the number of total exons and retained exons are given. Each retained exon remnant was assigned to class I or II, according to the strength of evidence for loss of their coding potential. The number of intragenic HCNEs from each host bystander gene is given as an indicator of potential regulatory content of the host gene’s introns.

^aBoth HDAC9 orthologs were lost from the synteny blocks of GRB target gene TWIST1 in zebrafish, which left two exonic remnants on zebrafish chromosome 19.

^bThree on chromosome 16.

^cIn the CHIC2 gene, there are two remnants on chr20:20493 k branch and they are identical in sequence and closely located in the chr20:23213 k branch in the Zv7 assembly, but both on the same branch are mapped to the same position in Zv8 assembly, which we considered as a Zv7 assembly error, and reported only one from each branch.