Table 1.
Endogenous zebrafish and plant genes targeted by CoDA ZFNs
| Gene name | Organism | Target site | Mutant alleles/ Total alleles | Mutation frequency |
|---|---|---|---|---|
| Dcl4a | Soybean | TGCTTCATCacaatGGAGATGAT | 6/32 | 18.8% |
| Dcl4b | Soybean | TGCTTCATCacaatGGAGATGAT | 3/28 | 10.7% |
| MPK8 | Arabidopsis | CTCCACAACatcagGATGACGAA | 7/83 | 8.4% |
| MPK11 | Arabidopsis | CTCTTCGTCctatcgGCAGAGGCG | 3/90 | 3.3% |
| MKK9 | Arabidopsis | GCCAGCGACggtggtGGTGGTGGC | 3/95 | 3.2% |
| MPK15 | Arabidopsis | TTCTTCATCcagatGTTGTTGAG | 2/73 | 2.7% |
| MAPKKK18 | Arabidopsis | CCCTTCCACaacaacGGAGAAGCT | 2/75 | 2.7% |
| GA3OX2 | Arabidopsis | AGCTACGCCgtagccGGAGACGCC | 1/94 | <=1.0% |
| MAPKKK1 | Arabidopsis | GGCACCTCCgatttcGTGGAGGAA | 0/190 | 0.0% |
| MAPKKK12 | Arabidopsis | TCCTCCACCgaatcGACGGCGCT | 0/187 | 0.0% |
| MAPKKK12 | Arabidopsis | TTCCTCCACcgaatcGACGGCGCT | 0/186 | 0.0% |
| MAPKKK4 | Arabidopsis | GTCTCCGCCtaggaGATGCAGAC | 0/190 | 0.0% |
| MPK15 | Arabidopsis | TGCTTCTTCatccaGATGTTGTT | 0/94 | 0.0% |
| MPK4 | Arabidopsis | CTCTTCGTCctatcgGTAGAGGCG | 0/190 | 0.0% |
| TZP | Arabidopsis | TTCGTCTTCgagtcGTCGTTGTT | 0/141 | 0.0% |
| actn1 | Zebrafish | GCCTTCTCCggggcGCAGAAGGT | 10/60 | 16.7% |
| rag2 | Zebrafish | ATCTTCTGCtccaggGGTGAAGGT | 4/52 | 7.7% |
| gad2 | Zebrafish | AGCCGCAGCtctcgGCTGTAGAC | 3/43 | 7.0% |
| lmna | Zebrafish | CTCTTCTCCcccagaGCTGTGGAG | 2/41 | 4.9% |
| apoeb | Zebrafish | CCCCTCAGCccagaTGGGAGGAG | 3/64 | 4.7% |
| trpm7 | Zebrafish | CACACCTGCacacaGATGCTGCT | 2/55 | 3.6% |
| grip1 | Zebrafish | GGCCACCTCcaccaGCAGCGGGC | 3/90 | 3.3% |
| pclo | Zebrafish | CCCCTCTCCtcaaaGCAGATGCA | 3/96 | 3.1% |
| jak3 | Zebrafish | GGCCCCACCaagcctGCTGGAGGA | 1/71 | <=1.0% |
| ago1 | Zebrafish | CTCTGCCGCcacctaGAGGATGGT | 1/96 | <=1.0% |
| slitrk1 | Zebrafish | GCCCACAGCaatggcGGAGCCGCC | 1/96 | <=1.0% |
| bmpr2a | Zebrafish | GACTTCCTCtctgtGCAGTCGGC | 1/117 | <=1.0% |
| bmpr2a | Zebrafish | ACCTCCTGCagtgtGAGGTTGTC | 0/156 | 0.0% |
| cnot1 | Zebrafish | GGCGTCCACgtacgaGCGGAGGAG | 0/93 | 0.0% |
| ctcf | Zebrafish | TTCCTCCTCctgatGCGGAGGCT | 0/96 | 0.0% |
| dicer1 | Zebrafish | TTCTGCAGCtcaatGGAGATGGT | 0/96 | 0.0% |
| dicer1 | Zebrafish | AGCTTCCTCcgccgGAAGTTGAG | 0/96 | 0.0% |
| drosha | Zebrafish | GTCCTCCTCatggcgGTCGATGGT | 0/96 | 0.0% |
| g6pcb | Zebrafish | TCCCACTGCtgattGTAGGTGGA | 0/134 | 0.0% |
| nedd4l | Zebrafish | AACCGCACCacacaGTGGAAGAG | 0/86 | 0.0% |
| nod2 | Zebrafish | AACTACAACattaggGCTGGAGGA | 0/103 | 0.0% |
| rag1 | Zebrafish | GTCCTCCCCttcaaGTCGAATAG | 0/91 | 0.0% |
| th2 | Zebrafish | CTCCTCCTCaaacacGAAGCTGTC | 0/142 | 0.0% |
| tp53 | Zebrafish | AGCAGCTGCatgggGGGGATGAA | 0/107 | 0.0% |
Target sites within each gene are written 5’ to 3’ with the two half-sites targeted by the zinc finger arrays shown in upper case letters and the intervening spacer sequence shown in lower case. Sequences of CoDA ZFN-induced zebrafish and plant gene mutations are shown in Supplementary Figs. 3 and 4, respectively.