Appendix A
Table A1.
Transcript identification and quantification for the ABCA4 variant NM_000350.2:c.573C>T for reference (WT) and variant (MT) minigenes (construct RHO_minigene_ABCA4_int4-6). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A1.
Transcript identification and quantification for the ABCA4 variant NM_000350.2:c.573C>T for reference (WT) and variant (MT) minigenes (construct RHO_minigene_ABCA4_int4-6). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-ABCA4_ex5-ABCA4_ex6-RHO_ex5 | 445 bp | 86.62 | 91.87 | 5.25 | 9395 | 7564 | WT |
T2 | RHO_ex3-RHO_ex5 | 119 bp | 8.04 | 3.52 | −4.52 | 872 | 290 | RHO exs |
T3 | RHO_ex3-ABCA4_ex6-RHO_ex5 | 317 bp | 1.65 | 1.15 | −0.5 | 179 | 95 | ex5 skip |
T4 | RHO_ex3-ABCA4_ex5-RHO_ex5 | 247 bp | 1.12 | 0.56 | −0.56 | 121 | 46 | ex6 skip |
Figure A1.
Functional characterization of the ABCA4 variant NM_000350.2:c.573C>T using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A1.
Functional characterization of the ABCA4 variant NM_000350.2:c.573C>T using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A2.
Transcript identification and quantification for the ABCA4 variant NM_000350.2:c.5586T>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_ABCA4_int38-41). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A2.
Transcript identification and quantification for the ABCA4 variant NM_000350.2:c.5586T>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_ABCA4_int38-41). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-ABCA4_ex39-ABCA4_ex40-ABCA4_ex41-RHO_ex5 | 494 bp | 47.64 | 46.9 | −0.74 | 747 | 507 | WT |
T2 | RHO_ex3-ABCA4_ex40-ABCA4_ex41-RHO_ex5 | 370 bp | 32.85 | 23.41 | −9.44 | 515 | 253 | ex39 skip |
T3 | RHO_ex3-ABCA4_ex39-ABCA4_int39-ABCA4_ex40-ABCA4_ex41-RHO_ex5 | 826 bp | 9.18 | 8.14 | −1.04 | 144 | 88 | int39 retention |
T4 | RHO_ex3-ABCA4_ex41-RHO_ex5 | 240 bp | 4.97 | 5.37 | 0.4 | 78 | 58 | ex39-40 skip |
T5 | RHO_ex3-ABCA4_ex39-ABCA4_ex41-RHO_ex5 | 364 bp | 0.89 | 0.74 | −0.15 | 14 | 8 | ex40 skip |
T6 | RHO_ex3-RHO_ex5 | 119 bp | 0 | 4.44 | 4.44 | 0 | 48 | RHO exs |
T7 | RHO_ex3-ABCA4_pe38a-ABCA4_ex39-ABCA4_ex40-ABCA4_ex41-RHO_ex5 | 688 bp | 0 | 0.56 | 0.56 | 0 | 6 | pe38a |
Figure A2.
Functional characterization of the ABCA4 variant NM_000350.2:c.5586T>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A2.
Functional characterization of the ABCA4 variant NM_000350.2:c.5586T>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A3.
Transcript identification and quantification for the ATF6 variant NM_007348.3:c.1096-15G>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_ATF6_int8-9). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A3.
Transcript identification and quantification for the ATF6 variant NM_007348.3:c.1096-15G>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_ATF6_int8-9). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-RHO_ex5 | 119 bp | 66.85 | 62.15 | −4.7 | 2492 | 2507 | RHO exs |
T2 | RHO_ex3-ATF6_ex9-RHO_ex5 | 211 bp | 32.48 | 33.91 | 1.43 | 1211 | 1368 | WT |
T3 | RHO_ex3-ATF6_ex9long-RHO_ex5 | 224 bp | 0 | 2.83 | 2.83 | 0 | 114 | altAS_predicted |
Figure A3.
Functional characterization of the ATF6 variant NM_007348.3:c.1096-15G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A3.
Functional characterization of the ATF6 variant NM_007348.3:c.1096-15G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A4.
Transcript identification and quantification for the ATF6 variant NM_007348.3:c.1096-15G>A for reference (WT) and variant (MT) minigenes (construct ATF6_minigene_ex1-2-9). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A4.
Transcript identification and quantification for the ATF6 variant NM_007348.3:c.1096-15G>A for reference (WT) and variant (MT) minigenes (construct ATF6_minigene_ex1-2-9). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | ATF6_ex1-ATF6_ex2-ATF6_ex9 | 850 bp | 86.22 | 61.01 | −25.21 | 3476 | 2031 | WT |
T2 | ATF6_ex1-ATF6_int1-ATF6_ex2-ATF6_ex9 | 1450 bp | 2.41 | 1.32 | −1.09 | 97 | 44 | int1 retention |
T3 | unspliced | 2103 bp | 1.09 | 3.48 | 2.39 | 44 | 116 | unspliced |
T4 | ATF6_ex1-ATF6_ex2-ATF6_int2-ATF6_ex9 | 1450 bp | 0.87 | 10.85 | 9.98 | 35 | 361 | int2 retention |
T5 | ATF6_ex1-ATF6_ex2-ATF6_ex9long | 863 bp | 0 | 6.09 | 6.09 | 0 | 203 | altAS_ex9long |
T6 | ATF6_ex1-ATF6_ex2-ATF6_ex9verylong | 1176 bp | 0 | 3.03 | 3.03 | 0 | 101 | altAS_ex9long_2 |
T7 | ATF6_ex1-ATF6_ex2-ATF6_pe9 | 694 bp | 0 | 1.38 | 1.38 | 0 | 46 | ex9 skip + pe9a_BGH |
Figure A4.
Functional characterization of the ATF6 variant NM_007348.3:c.1096-15G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A4.
Functional characterization of the ATF6 variant NM_007348.3:c.1096-15G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A5.
Transcript identification and quantification for the ATF6 variant NM_007348.3:c.1534-9A>G for reference (WT) and variant (MT) minigenes (construct ATF6_minigene_ex1-2-13). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A5.
Transcript identification and quantification for the ATF6 variant NM_007348.3:c.1534-9A>G for reference (WT) and variant (MT) minigenes (construct ATF6_minigene_ex1-2-13). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | ATF6_ex1-ATF6_ex2-ATF6_ex13 | 795 bp | 87.46 | 6.88 | −80.58 | 2586 | 140 | WT |
T2 | ATF6_ex1-ATF6_int1-ATF6_ex2-ATF6_ex13 | 1395 bp | 1.69 | 0 | −1.69 | 50 | 0 | int1 retention |
T3 | ATF6_ex1-ATF6_ex2-ATF6_ex13long | 803 bp | 0 | 77.32 | 77.32 | 0 | 1574 | altAS_ex13long |
T4 | ATF6_ex1-ATF6_ex2-ATF6_int2_ATF6_ex13 | 1395 bp | 0 | 0.88 | 0.88 | 0 | 18 | int2 retention |
Figure A5.
Functional characterization of the ATF6 variant NM_007348.3:c.1534-9A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A5.
Functional characterization of the ATF6 variant NM_007348.3:c.1534-9A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A6.
Transcript identification and quantification for the CACNA1F variant M_005183.4:c.2239+5C>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_CACNA1F_int14-18). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A6.
Transcript identification and quantification for the CACNA1F variant M_005183.4:c.2239+5C>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_CACNA1F_int14-18). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 471 bp | 27.6 | 49.69 | 22.09 | 6922 | 15416 | ex16 skip + altAS_ex17long |
T2 | RHO_ex3-CACNA1F_ex15short-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 353 bp | 14.38 | 11.67 | −2.71 | 3608 | 3620 | altAS_ex15short + ex16 skip + altAS_ex17long |
T3 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex16-CACNA1F_ex17-CACNA1F_ex18-RHO_ex5 | 576 bp | 11.24 | 0 | −11.24 | 2820 | 0 | WT |
T4 | RHO_ex3-CACNA1F_ex15short-CACNA1F_ex16-CACNA1F_ex17-CACNA1F_ex18-RHO_ex5 | 458 bp | 7.48 | 0 | −7.48 | 1876 | 0 | altAS_ex15short |
T5 | RHO_ex3-CACNA1F_ex18-RHO_ex5 | 165 bp | 7.03 | 3.57 | −3.46 | 1763 | 1108 | ex15-17 skip |
T6 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex18-RHO_ex5 | 373 bp | 4.25 | 7.78 | 3.53 | 1065 | 2415 | ex16-17 skip |
T7 | RHO_ex3-RHO_ex5 | 119 bp | 4.24 | 1.24 | −3 | 1063 | 384 | RHO exs |
T8 | RHO_ex3-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 263 bp | 3.9 | 10.22 | 6.32 | 978 | 3172 | ex 15-16 skip + alt17long |
T9 | RHO_ex3-CACNA1F_ex15short-CACNA1F_ex18-RHO_ex5 | 255 bp | 2.4 | 1.5 | −0.9 | 602 | 465 | altAS_ex15short + ex16-17 skip |
T10 | RHO_ex3-CACNA1F_pe16-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 363 bp | 1.98 | 4.67 | 2.69 | 496 | 1449 | ex16 skip + int15 retention |
T11 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex16short-CACNA1F_ex17-CACNA1F_ex18-RHO_ex5 | 503 bp | 1.65 | 0 | −1.65 | 414 | 0 | altAS_ex16short |
T12 | RHO_ex3-CACNA1F_ex15short-CACNA1F_ex16short-CACNA1F_ex17-CACNA1F_ex18-RHO_ex5 | 385 bp | 1.16 | 0 | −1.16 | 292 | 0 | altAS_ex15short + altAS_ex16short |
T13 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex16-CACNA1F_ex18-RHO_ex5 | 494 bp | 1.05 | 0 | −1.05 | 264 | 0 | ex17 skip |
T14 | RHO_ex3-CACNA1F_pe16-CACNA1F_ex18-RHO_ex5 | 265 bp | 0.85 | 1.86 | 1.01 | 212 | 577 | ex16-17 skip + int15 retention |
T15 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex16short-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 552 bp | 0.77 | 0 | −0.77 | 192 | 0 | altAS_ex16short + altAS_ex17long |
T16 | RHO_ex3-CACNA1F_ex15short-CACNA1F_ex16-CACNA1F_ex18-RHO_ex5 | 401 bp | 0.72 | 0 | −0.72 | 180 | 0 | altAS_ex15short + ex17 skip |
T17 | RHO_ex3-CACNA1F_ex15-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 570 bp | 0.56 | 1.15 | 0.59 | 140 | 358 | ex16 skip + altAS_altDS_ex17long |
T18 | RHO_ex3-CACNA1F_ex15short-CACNA1F_ex16short-CACNA1F_ex17long-CACNA1F_ex18-RHO_ex5 | 434 bp | 0.55 | 0 | −0.55 | 139 | 0 | altAS_ex15short + altAS_ex16short + altAS_ex17long |
Figure A6.
Functional characterization of the CACNA1F variant NM_005183.4:c.2239+5C>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A6.
Functional characterization of the CACNA1F variant NM_005183.4:c.2239+5C>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A7.
Transcript identification and quantification for the CHM variant NM_000390.4:c.1413G>C for reference (WT) and variant (MT) minigenes (construct RHO_minigene_CHM_int9-11). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A7.
Transcript identification and quantification for the CHM variant NM_000390.4:c.1413G>C for reference (WT) and variant (MT) minigenes (construct RHO_minigene_CHM_int9-11). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-CHM_ex10-CHM_ex11-RHO_ex5 | 288 bp | 85.14 | 0 | −85.14 | 9278 | 0 | WT |
T2 | RHO_ex3-CHM_ex10-RHO_ex5 | 224 bp | 12.75 | 98.68 | 85.93 | 1390 | 8198 | ex11 skip |
Figure A7.
Functional characterization of the CHM variant NM_000390.4:c.1413G>C using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A7.
Functional characterization of the CHM variant NM_000390.4:c.1413G>C using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A8.
Transcript identification and quantification for the FZD4 variant NM_012193.4:c.313A>G for reference (WT) and variant (MT) minigenes (construct FZD4_minigene_ex1-2). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A8.
Transcript identification and quantification for the FZD4 variant NM_012193.4:c.313A>G for reference (WT) and variant (MT) minigenes (construct FZD4_minigene_ex1-2). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | FZD4_ex1-FZD4_ex2 | 2248 bp | 52.92 | 54.75 | 1.83 | 232 | 225 | WT |
Figure A8.
Functional characterization of the FZD4 variant NM_012193.4:c.313A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A8.
Functional characterization of the FZD4 variant NM_012193.4:c.313A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A9.
Transcript identification and quantification for the IMPG2 variant NM_016247.4:c.3423-7_3423-4del for reference (WT) and variant (MT) minigenes (construct RHO_minigene_IMPG2_int15-18). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A9.
Transcript identification and quantification for the IMPG2 variant NM_016247.4:c.3423-7_3423-4del for reference (WT) and variant (MT) minigenes (construct RHO_minigene_IMPG2_int15-18). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-RHO_ex5 | 119 bp | 51.6 | 45.67 | −5.93 | 36897 | 44149 | RHO exs |
T2 | RHO_ex3-IMPG2_ex18-RHO_ex5 | 199 bp | 36.68 | 52.24 | 15.56 | 26230 | 50496 | ex16-17 skip |
T3 | RHO_ex3-IMPG2_ex17-IMPG2_ex18-RHO_ex5 | 410 bp | 8.8 | 0 | −8.8 | 6293 | 0 | ex16 skip |
T4 | RHO_ex3-IMPG2_ex16-IMPG2_ex17-IMPG2_ex18-RHO_ex5 | 599 bp | 1.06 | 0 | −1.06 | 758 | 0 | WT |
T5 | RHO_ex3-IMPG2_ex16-IMPG2_ex18-RHO_ex5 | 388 bp | 0 | 0.62 | 0.62 | 0 | 604 | ex17 skip |
Figure A9.
Functional characterization of the IMPG2 variant NM_016247.4:c.3423-7_3423-4del using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A9.
Functional characterization of the IMPG2 variant NM_016247.4:c.3423-7_3423-4del using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A10.
Transcript identification and quantification for the IMPG2 variant NM_016247.4:c.3423-7_3423-4del for reference (WT) and variant (MT) minigenes (construct RHO_minigene_IMPG2_int16-17). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A10.
Transcript identification and quantification for the IMPG2 variant NM_016247.4:c.3423-7_3423-4del for reference (WT) and variant (MT) minigenes (construct RHO_minigene_IMPG2_int16-17). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-IMPG2_ex17-RHO_ex5 | 330 bp | 56.11 | 9.15 | −46.96 | 9344 | 870 | WT |
T2 | RHO_ex3-RHO_ex5 | 119 bp | 42.19 | 67.64 | 25.45 | 7026 | 6431 | ex17 skip |
T3 | RHO_ex3-IMPG2_ex17long-RHO_ex5 | 410 bp | 0 | 18.59 | 18.59 | 0 | 1767 | altAS_ex17long |
T4 | RHO_ex3-IMPG2_pe16a-IMPG2_ex17long-RHO_ex5 | 540 bp | 0 | 1.36 | 1.36 | 0 | 129 | pe16a + altAS_ex17long |
T5 | RHO_ex3-IMPG2_ex17short-RHO_ex5 | 201 bp | 0 | 0.96 | 0.96 | 0 | 91 | altAS_ex17short |
T6 | RHO_ex3-IMPG2_pe16a-RHO_ex5 | 249 bp | 0 | 0.75 | 0.75 | 0 | 71 | pe16a + ex17 skip |
Figure A10.
Functional characterization of the IMPG2 variant NM_016247.4:c.3423-7_3423-4del using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A10.
Functional characterization of the IMPG2 variant NM_016247.4:c.3423-7_3423-4del using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A11.
Transcript identification and quantification for the OCA2 variant NM_000275.3:c.574-53C>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_OCA2_int5-7). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A11.
Transcript identification and quantification for the OCA2 variant NM_000275.3:c.574-53C>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_OCA2_int5-7). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-RHO_ex5 | 119 bp | 80.87 | 73.68 | −7.19 | 89,903 | 58,923 | RHO exs |
T2 | RHO_ex3-OCA2_ex6-OCA2_ex7-RHO_ex5 | 353 bp | 17.6 | 24.91 | 7.31 | 19,560 | 19,921 | WT |
Figure A11.
Functional characterization of the OCA2 variant NM_000275.3:c.574-53C>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A11.
Functional characterization of the OCA2 variant NM_000275.3:c.574-53C>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A12.
Transcript identification and quantification for the PDE6C variant NM_006204.3:c.864+1G>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_PDE6C_int3-4). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A12.
Transcript identification and quantification for the PDE6C variant NM_006204.3:c.864+1G>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_PDE6C_int3-4). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-PDE6C_ex4-RHO_ex5 | 260 bp | 97.99 | 0 | −97.99 | 5617 | 0 | WT |
T2 | RHO_ex3-PDE6C_ex4long1-RHO_ex5 | 388 bp | 0 | 65.48 | 65.48 | 0 | 4616 | alDS_ex4long |
T3 | RHO_ex3-PDE6C_ex4short-RHO_ex5 | 197 bp | 0 | 28.64 | 28.64 | 0 | 2019 | alDS_ex4short |
T4 | RHO_ex3-RHO_ex5 | 119 bp | 0 | 2.65 | 2.65 | 0 | 187 | RHO exs |
T5 | RHO_ex3-PDE6C_ex4long2-RHO_ex5 | 352 bp | 0 | 1.12 | 1.12 | 0 | 79 | alDS_ex4long |
T6 | RHO_ex3-PDE6C_ex4long3-RHO_ex5 | 394 bp | 0 | 1.01 | 1.01 | 0 | 71 | alDS_ex4long |
Figure A12.
Functional characterization of the PDE6C variant NM_006204.3:c.864+1G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A12.
Functional characterization of the PDE6C variant NM_006204.3:c.864+1G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A13.
Transcript identification and quantification for the POC1B variant NM_172240.2:c.677-2A>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_POC1B_int6-7). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A13.
Transcript identification and quantification for the POC1B variant NM_172240.2:c.677-2A>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_POC1B_int6-7). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-POC1B_ex7-RHO_ex5 | 253 bp | 92.25 | 0 | −92.25 | 4736 | 0 | WT |
T2 | RHO_ex3-RHO_ex5 | 119 bp | 3.23 | 8.29 | 5.06 | 166 | 387 | RHO exs |
T3 | RHO_ex3-POC1B_ex7short2-RHO_ex5 | 193 bp | 1.81 | 4.46 | 2.65 | 93 | 208 | altAS_ex7short |
T4 | RHO_ex3-POC1B_ex7short1-RHO_ex5 | 161 bp | 1.81 | 0 | −1.81 | 93 | 0 | altDS_ex7short |
T5 | RHO_ex3-POC1B_ex7short3-RHO_ex5 | 246 bp | 0.51 | 86.24 | 85.73 | 26 | 4025 | altAS_ex7short |
Figure A13.
Functional characterization of the POC1B variant NM_172240.2:c.677-2A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A13.
Functional characterization of the POC1B variant NM_172240.2:c.677-2A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A14.
Transcript identification and quantification for the POC1B variant NM_172240.2:c.1033-327T>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_POC1B_int9-10). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A14.
Transcript identification and quantification for the POC1B variant NM_172240.2:c.1033-327T>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_POC1B_int9-10). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-POC1B_ex10-RHO_ex5 | 200 bp | 91.3 | 43.3 | −48 | 5355 | 5773 | WT |
T2 | RHO_ex3-POC1B_pe9a-POC1B_ex10-RHO_ex5 | 327 bp | 4.65 | 0 | −4.65 | 273 | 0 | pe9a |
T3 | RHO_ex3-POC1B_ex10short-RHO_ex5 | 137 bp | 1.5 | 0 | −1.5 | 88 | 0 | altDS_ex10short |
T4 | RHO_ex3-POC1B_pe9b-POC1B_ex10-RHO_ex5 | 228 bp | 0 | 38.32 | 38.32 | 0 | 5109 | pe9b |
T5 | RHO_ex3-POC1B_pe9a_long-POC1B_ex10-RHO_ex5 | 347 bp | 0 | 5.93 | 5.93 | 0 | 790 | pe9a |
T6 | RHO_ex3-POC1B_ex9alt-POC1B_ex10-RHO_ex5 | 223 bp | 0 | 4.09 | 4.09 | 0 | 545 | ex9 of NR_037659.2 |
T7 | RHO_ex3-POC1B_pe9b-POC1B_ex10short-RHO_ex5 | 165 bp | 0 | 2.24 | 2.24 | 0 | 299 | pe9b/altAS_ex10short |
T8 | RHO_ex3-POC1B_ex10short2-RHO_ex5 | 167 bp | 0 | 0.9 | 0.9 | 0 | 120 | altAS_ex10short |
T9 | RHO_ex3-RHO_ex5 | 119 bp | 0 | 0.68 | 0.68 | 0 | 90 | RHO exs |
Figure A14.
Functional characterization of the POC1B variant NM_172240.2:c.1033-327T>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A14.
Functional characterization of the POC1B variant NM_172240.2:c.1033-327T>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A15.
Transcript identification and quantification for the PROM1 variant NM_006017.3:c.2358C>T for reference (WT) and variant (MT) minigenes (construct RHO_minigene_PROM1_int20-23). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A15.
Transcript identification and quantification for the PROM1 variant NM_006017.3:c.2358C>T for reference (WT) and variant (MT) minigenes (construct RHO_minigene_PROM1_int20-23). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-PROM1_ex21-PROM1_ex22-PROM1_ex23-RHO_ex5 | 362 bp | 94.48 | 55.35 | −39.13 | 73,805 | 47,675 | WT |
T2 | RHO_ex3-PROM1_ex21long-PROM1_ex22-PROM1_ex23-RHO_ex5 | 454 bp | 1.13 | 0 | −1.13 | 879 | 0 | altAS_ex21long |
T3 | RHO_ex3-PROM1_ex21long-PROM1_ex22-PROM1_ex23-RHO_ex5 | 441 bp | 0.6 | 0 | −0.6 | 470 | 0 | altAS_ex21long |
T4 | RHO_ex3-PROM1_ex21-PROM1_ex22-RHO_ex5 | 269 bp | 0 | 40.92 | 40.92 | 0 | 35,256 | ex23 skip |
T5 | RHO_ex3-RHO_ex5 | 119 bp | 0 | 0.56 | 0.56 | 0 | 484 | RHO exs |
Figure A15.
Functional characterization of the PROM1 variant NM_006017.3:c.2358C>T using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A15.
Functional characterization of the PROM1 variant NM_006017.3:c.2358C>T using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A16.
Transcript identification and quantification for the PROM1 variant NM_006017.3:c.2490-2A>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_PROM1_int23-26). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A16.
Transcript identification and quantification for the PROM1 variant NM_006017.3:c.2490-2A>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_PROM1_int23-26). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-PROM1_ex24-RHO_ex5 | 235 bp | 75.46 | 76.79 | 1.33 | 2414 | 1105 | ex25-26 skip |
T2 | RHO_ex3-RHO_ex5 | 119 bp | 13.66 | 9.94 | −3.72 | 437 | 143 | RHO exs |
T3 | RHO_ex3-PROM1_ex24-PROM1_ex26-RHO_ex5 | 304 bp | 5.28 | 11.95 | 6.67 | 169 | 172 | ex25 skip |
T4 | RHO_ex3-PROM1_ex24-PROM1_ex25-PROM1_ex26-RHO_ex5 | 328 bp | 3.69 | 0 | −3.69 | 118 | 0 | WT |
Figure A16.
Functional characterization of the PROM1 variant NM_006017.3:c.2490-2A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A16.
Functional characterization of the PROM1 variant NM_006017.3:c.2490-2A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A17.
Transcript identification and quantification for the REEP6 variant NM_001329556.3:c.517G>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_REEP6_int1-5). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A17.
Transcript identification and quantification for the REEP6 variant NM_001329556.3:c.517G>A for reference (WT) and variant (MT) minigenes (construct RHO_minigene_REEP6_int1-5). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-REEP6_ex2-REEP6_ex3-REEP6_ex4-RHO_ex5 | 521 bp | 66.55 | 10.64 | −55.91 | 1148 | 425 | WT |
T2 | RHO_ex3-REEP6_ex2-REEP6_ex3-REEP6_ex4short-RHO_ex5 | 489 bp | 10.38 | 1.38 | −9 | 179 | 55 | altAS_ex4short |
T3 | RHO_ex3-REEP6_ex2-REEP6_int2-REEP6_ex3-REEP6_ex4-RHO_ex5 | 602 bp | 10.03 | 0.7 | −9.33 | 173 | 28 | int2 retention |
T4 | RHO_ex3-RHO_ex5 | 119 bp | 5.39 | 10.46 | 5.07 | 93 | 418 | RHO exs |
T5 | RHO_ex3-REEP6_ex2-REEP6_ex3-REEP6_int3-REEP6_ex4-RHO_ex5 | 1198 bp | 0.99 | 0 | −0.99 | 17 | 0 | int3 retention |
T6 | RHO_ex3-REEP6_ex2-REEP6_ex3-RHO_ex5 | 352 bp | 0.87 | 56.33 | 55.46 | 15 | 2251 | ex4 skip |
T7 | RHO_ex3-REEP6_ex2-REEP6_int2-REEP6_ex3-REEP6_ex4short-RHO_ex5 | 570 bp | 0.81 | 0 | −0.81 | 14 | 0 | int2 retention + altAS_ex4short |
T8 | RHO_ex3-REEP6_ex2-REEP6_ex3-REEP6_ex4long1-RHO_ex5 | 564 bp | 0 | 10.41 | 10.41 | 0 | 416 | altDS_ex4long |
T9 | RHO_ex3-REEP6_ex2-REEP6_int2-REEP6_ex3-RHO_ex5 | 433 bp | 0 | 3.43 | 3.43 | 0 | 137 | int2 retention + ex4 skip |
T10 | RHO_ex3-REEP6_ex2-RHO_ex5 | 213 bp | 0 | 1.73 | 1.73 | 0 | 69 | ex3-4 skip |
T11 | RHO_ex3-REEP6_ex2-REEP6_ex3-REEP6_ex4long2-RHO_ex5 | 532 bp | 0 | 1.08 | 1.08 | 0 | 43 | altAS-DS_ex4long |
T12 | RHO_ex3-REEP6_ex2-REEP6_int2-REEP6_ex3-REEP6_ex4long1-RHO_ex5 | 645 bp | 0 | 0.58 | 0.58 | 0 | 23 | int2 retention + altDS_ex4long |
Figure A17.
Functional characterization of the REEP6 variant NM_001329556.3:c.517G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A17.
Functional characterization of the REEP6 variant NM_001329556.3:c.517G>A using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A18.
Transcript identification and quantification for the RPGR variant NM_001034853.1:c.1415-9A>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_RPGR_int10-13). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A18.
Transcript identification and quantification for the RPGR variant NM_001034853.1:c.1415-9A>G for reference (WT) and variant (MT) minigenes (construct RHO_minigene_RPGR_int10-13). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-RPGR_ex11-RPGR_ex12-RPGR_ex13-RHO_ex5 | 446 bp | 56.04 | 0.88 | −55.16 | 1943 | 30 | WT |
T2 | RHO_ex3-RPGR_ex11short1-RPGR_ex12-RPGR_ex13-RHO_ex5 | 355 bp | 28.38 | 1.35 | −27.03 | 984 | 46 | altAS_ex11short |
T3 | RHO_ex3-RPGR_ex11short2-RPGR_ex12-RPGR_ex13-RHO_ex5 | 302 bp | 2.65 | 0 | −2.65 | 92 | 0 | altAS_ex11short |
T4 | RHO_ex3-RPGR_ex11short1-RPGR_ex13-RHO_ex5 | 263 bp | 2.48 | 7.54 | 5.06 | 86 | 257 | altAS_ex11short + ex12 skip |
T5 | RHO_ex3-RPGR_ex11-RPGR_ex12short-RPGR_ex13-RHO_ex5 | 434 bp | 2.13 | 0 | −2.13 | 74 | 0 | altAS_ex12short |
T6 | RHO_ex3-RPGR_ex11-RPGR_ex13-RHO_ex5 | 354 bp | 2.08 | 5.58 | 3.5 | 72 | 190 | ex12 skip |
T7 | RHO_ex3-RHO_ex5 | 119 bp | 1.59 | 6.43 | 4.84 | 55 | 219 | RHO exs |
T8 | RHO_ex3-RPGR_ex11short1-RPGR_ex12short-RPGR_ex13-RHO_ex5 | 343 bp | 0.89 | 0 | −0.89 | 31 | 0 | altAS_ex11short + altAS_ex12short |
T9 | RHO_ex3-RPGR_ex11short1-RPGR_ex12long-RPGR_ex13-RHO_ex5 | 363 bp | 0 | 38.56 | 38.56 | 0 | 1314 | altAS_ex11short + altAS_ex12long |
T10 | RHO_ex3-RPGR_ex11-RPGR_ex12long-RPGR_ex13-RHO_ex5 | 454 bp | 0 | 29.15 | 29.15 | 0 | 993 | altAS_ex12long |
T11 | RHO_ex3-RPGR_ex11short2-RPGR_ex12long-RPGR_ex13-RHO_ex5 | 310 bp | 0 | 2.79 | 2.79 | 0 | 95 | altAS_ex11short + altAS_ex12long |
T12 | RHO_ex3-RPGR_ex11-RHO_ex5 | 288 bp | 0 | 0.73 | 0.73 | 0 | 25 | ex12-13 skip |
T13 | RHO_ex3-RPGR_ex11short2-RPGR_ex13-RHO_ex5 | 210 bp | 0 | 0.7 | 0.7 | 0 | 24 | altAS_ex11short + ex12 skip |
T14 | RHO_ex3-RPGR_ex11short1-RHO_ex5 | 197 bp | 0 | 0.65 | 0.65 | 0 | 22 | altAS_ex11short + ex12-13 skip |
Figure A18.
Functional characterization of the RPGR variant NM_001034853.1:c.1415-9A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A18.
Functional characterization of the RPGR variant NM_001034853.1:c.1415-9A>G using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A19.
Transcript identification and quantification for the TIMP3 variant NM_000362.4:c.205-3117T>C for reference (WT) and variant (MT) minigenes (construct RHO_minigene_TIMP3_int1-3). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A19.
Transcript identification and quantification for the TIMP3 variant NM_000362.4:c.205-3117T>C for reference (WT) and variant (MT) minigenes (construct RHO_minigene_TIMP3_int1-3). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on transcript |
---|
T1 | RHO_ex3-TIMP3_ex2-TIMP3_ex3-RHO_ex5 | 314 bp | 90.84 | 91 | 0.16 | 94’674 | 59’457 | WT |
T2 | RHO_ex3--TIMP3_pe2a_TIMP3_ex2-TIMP3_ex3-RHO_ex5 | 363 bp | 7.22 | 7.02 | −0.2 | 7520 | 4588 | pe2a |
Figure A19.
Functional characterization of the TIMP3 variant NM_000362.4:c.205-3117T>C using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A19.
Functional characterization of the TIMP3 variant NM_000362.4:c.205-3117T>C using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Table A20.
Transcript identification and quantification for the USH2A variant NM_206933.2:c.652-22287T>C for reference (WT) and variant (MT) minigenes (construct RHO_minigene_USH2A_int3). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
Table A20.
Transcript identification and quantification for the USH2A variant NM_206933.2:c.652-22287T>C for reference (WT) and variant (MT) minigenes (construct RHO_minigene_USH2A_int3). The table lists the transcripts identified, along with their characteristics, such as length, their relative abundance in reference (WT) and variant (MT) minigenes, the difference (delta) in relative abundance between MT and WT sequencing results, the absolute number of reads representing each transcript, and the effect on the transcript. The table is sorted by relative abundance.
| Transcript | Length | WT (%) | MT (%) | Δ MT-WT (%) | Counts WT | Counts MT | Effect on Transcript |
---|
T1 | RHO_ex3-RHO_ex5 | 119 bp | 98.69 | 98.06 | −0.63 | 56,927 | 87,450 | WT |
T2 | RHO_ex3-USH2A_pe4a-RHO_ex5 | 158 bp | 0.95 | 1.41 | 0.46 | 546 | 1253 | pe4a |
Figure A20.
Functional characterization of the USH2A variant NM_206933.2:c.652-22287T>C using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.
Figure A20.
Functional characterization of the USH2A variant NM_206933.2:c.652-22287T>C using minigene assays. The panel shows an IGV screenshot highlighting the construct’s characteristics, followed by the coverage plots for the reference (WT) and variant (MT) minigenes. An overview of each transcript (name T#) identified and its relative abundance in WT and MT can be seen underneath the coverage plots. The green transcript represents the expected reference (WT) transcript.