Table 1 Ranking of genomic landscape of IRD genes according to gene size, number of total associated repeats, Alu repeats, LINE and LTR repeats, and segmental duplications, together with the number of CNVs according to literature and DGV
Gene size | Total repeats | Alu repeats | LINE and LTR repeats | Segmental duplications | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | Lit. | DGV | Gene | Lit. | DGV | Gene | Lit. | DGV | Gene | Lit. | DGV | Gene | Lit. | DGV |
EYS | 24 | 9,470 | EYS | 24 | 9,470 | OPA3 | 0 | 27 | EYS | 24 | 9,470 | HMX1 | 0 | 10 |
PCDH15 | 15 | 6,344 | PCDH15 | 15 | 6,344 | NMNAT1 | 2 | 1 | PCDH15 | 15 | 6,344 | CLN3 | 515 | 18 |
USH2A | 57 | 598 | WDPCP | 0 | 174 | CLN3 | 515 | 18 | WDPCP | 0 | 174 | NPHP1 | 75 | 445 |
WDPCP | 0 | 174 | ADGRV1 | 4 | 192 | PRPF8 | 0 | 6 | USH2A | 57 | 598 | CA4 | 0 | 10 |
ADGRV1 | 4 | 192 | CDH23 | 3 | 740 | CTNNA1 | 0 | 117 | ADGRV1 | 4 | 192 | SDCCAG8 | 1 | 123 |
RIMS1 | 0 | 1945 | USH2A | 57 | 598 | PCYT1A | 0 | 420 | BBS9 | 7 | 897 | ABCC6 | 235 | 141 |
BBS9 | 7 | 897 | BBS9 | 7 | 897 | PNPLA6 | 0 | 3 | NBAS | 0 | 59 | OPN1SW | 0 | 100 |
HMCN1 | 0 | 723 | ZNF423 | 0 | 287 | CRX | 1 | 60 | RIMS1 | 0 | 1,945 | BBS4 | 13 | 10 |
CDH23 | 3 | 740 | CTNNA1 | 0 | 117 | PRPF3 | 0 | 3 | INVS | 0 | 53 | IMPDH1 | 0 | 24 |
NBAS | 0 | 59 | OPA3 | 0 | 27 | CDH3 | 1 | 44 | ALMS1 | 5 | 73 | ACBD5 | 0 | 8 |
ZNF423 | 0 | 287 | CRX | 1 | 60 | C12ORF65 | 0 | 6 | HMCN1 | 0 | 723 | GPR179 | 0 | 2 |
CTNNA1 | 0 | 117 | TTLL5 | 0 | 404 | DHDDS | 0 | 11 | GPR125 | 0 | 143 | CIB2 | 0 | 7 |
TTLL5 | 0 | 404 | NBAS | 0 | 59 | RAX2 | 0 | 2 | TEAD1 | 0 | 148 | ADIPOR1 | 0 | 0 |
TEAD1 | 0 | 148 | CLN3 | 515 | 18 | ROM1 | 0 | 6 | ZNF423 | 0 | 287 | TRPM1 | 7 | 77 |
SDCCAG8 | 1 | 123 | ABCC6 | 235 | 141 | PRPH2 | 1 | 4 | TTLL5 | 0 | 404 | PCDH15 | 15 | 6,344 |
COL11A1 | 7 | 60 | HK1 | 0 | 113 | CEP250 | 0 | 4 | CDH23 | 3 | 740 | RGS9 | 0 | 2 |
ALMS1 | 5 | 73 | CDH3 | 1 | 44 | FAM161A | 0 | 13 | PLA2G5 | 0 | 77 | RBP3 | 0 | 24 |
AHI1 | 1 | 96 | KIAA1549 | 0 | 69 | ARL3 | 0 | 2 | CC2D2A | 1 | 149 | LCA5 | 1 | 8 |
CRB1 | 0 | 43 | DHDDS | 0 | 11 | ABCC6 | 235 | 141 | CTNNA1 | 0 | 117 | SLC24A1 | 0 | 3 |
INVS | 0 | 53 | DFNB31 | 0 | 53 | KIF11 | 0 | 5 | MYO7A | 6 | 85 | CRB1 | 0 | 43 |
ATF6 | 0 | 43 | PCYT1A | 0 | 420 | PRCD | 0 | 6 | ATF6 | 0 | 43 | NR2F1 | 3 | 21 |
CNGB3 | 0 | 45 | RIMS1 | 0 | 1,945 | ZNF408 | 0 | 0 | CNGB3 | 0 | 45 | CDHR1 | 0 | 3 |
ADAMTS18 | 0 | 40 | HMCN1 | 0 | 723 | RPGRIP1 | 1 | 2547 | KIZ | 0 | 120 | RGR | 0 | 4 |
CHM | 30 | 435 | PDE6A | 1 | 45 | CLUAP1 | 0 | 2 | TRPM1 | 7 | 77 | CSPP1 | 0 | 55 |
LAMA1 | 1 | 55 | INVS | 0 | 53 | SEMA4A | 0 | 1 | PITPNM3 | 0 | 20 | POMGNT1 | 0 | 19 |
GPR125 | 0 | 143 | KIF11 | 0 | 5 | KIAA1549 | 0 | 69 | TTC8 | 0 | 20 | PRPF6 | 0 | 67 |
TRPM1 | 7 | 77 | PNPLA6 | 0 | 3 | NYX | 5 | 5 | MERTK | 7 | 90 | PCYT1A | 0 | 420 |
IMPG1 | 0 | 88 | FAM161A | 0 | 13 | GPR179 | 0 | 2 | PROM1 | 0 | 7 | NPHP4 | 1 | 163 |
KIAA1549 | 0 | 69 | ALMS1 | 5 | 73 | HK1 | 0 | 113 | CEP290 | 2 | 10 | CNNM4 | 2 | 171 |
CERKL | 0 | 55 | CEP250 | 0 | 4 | BBS1 | 6 | 4 | CAPN5 | 1 | 56 | RPGRIP1L | 0 | 145 |
