Table 1.
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.