Table 1 Skipped exon (SE) evidence of ABCB1 transcripts detected in transcriptomes from KB-C2-k.o.cdk6, KB-C2-k.o.cdk4, KB-C2-110α, KB-C2-110β as compared with KB-C2 transcriptome
(I) KB-C2-k.o.cdk6 vs KB-C2 | ||||||||||||
AS ID | Gene ID | Gene name | Novel AS | Chr | Diff significant | P Value Junction Count Only | Exon Start (0 base) | Exon End | Upstream ES | Upstream EE | Downstream ES | Downstream EE |
SE_46658 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87516508 | 87516665 | 87515227 | 87515428 | 87519325 | 87519466 |
SE_46659 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87536457 | 87536541 | 87531293 | 87531497 | 87539267 | 87539345 |
SE_46657 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87505896 | 87506043 | 87502690 | 87504449 | 87509274 | 87509481 |
SE_46669 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.9038720596 | 87602959 | 87603140 | 87600812 | 87601078 | 87713160 | 87713295 |
SE_46668 | ENSG00000085563 | ABCB1 | yes | 7 | yes | 7.74577644824E-006 | 87601966 | 87603140 | 87600754 | 87601078 | 87605645 | 87605775 |
SE_46663 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550724 | 87550838 | 87550467 | 87550578 | 87553760 | 87553932 |
SE_46662 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550170 | 87550296 | 87549850 | 87550054 | 87550467 | 87550578 |
SE_46661 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87549347 | 87549518 | 87545862 | 87546024 | 87549850 | 87550054 |
SE_46660 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87541356 | 87541464 | 87539267 | 87539345 | 87544128 | 87544275 |
SE_46667 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87595765 | 87595814 | 87585511 | 87585680 | 87600116 | 87600190 |
SE_46666 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87595765 | 87595814 | 87505896 | 87506043 | 87600116 | 87600190 |
SE_46665 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.0682123258 | 87566784 | 87566976 | 87566069 | 87566241 | 87570171 | 87570223 |
SE_46664 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.4481719285 | 87566069 | 87566241 | 87561262 | 87561387 | 87570171 | 87570223 |
SE_46670 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.7879487815 | 87605645 | 87605775 | 87600754 | 87601078 | 87713160 | 87713294 |
(II) KB-C2-k.o.cdk4 vs KB-C2 | ||||||||||||
AS ID | Gene ID | Gene name | Novel AS | Chr | Diff significant | P Value Junction Count Only | Exon Start (0 base) | Exon End | Upstream ES | Upstream EE | Downstream ES | Downstream EE |
SE_47404 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.1867192198 | 87566784 | 87566976 | 87566069 | 87566241 | 87570171 | 87570223 |
SE_47405 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87595765 | 87595814 | 87585511 | 87585680 | 87600116 | 87600190 |
SE_47406 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.4757658641 | 87601966 | 87603140 | 87600754 | 87601078 | 87605645 | 87605775 |
SE_47407 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.1348013017 | 87602959 | 87603140 | 87600812 | 87601078 | 87713160 | 87713295 |
SE_47400 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87549347 | 87549518 | 87545862 | 87546024 | 87549850 | 87550054 |
SE_47401 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550170 | 87550296 | 87549850 | 87550054 | 87550467 | 87550578 |
SE_47402 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550724 | 87550838 | 87550467 | 87550578 | 87553760 | 87553932 |
SE_47403 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.3242107276 | 87566069 | 87566241 | 87561262 | 87561387 | 87570171 | 87570223 |
SE_47408 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.0695066227 | 87605645 | 87605775 | 87600754 | 87601078 | 87713160 | 87713294 |
SE_47409 | ENSG00000085563 | ABCB1 | no | 7 | yes | 2.4192194914E-009 | 87605645 | 87605775 | 87601966 | 87603140 | 87713160 | 87713294 |
SE_47397 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87519325 | 87519466 | 87516508 | 87516665 | 87520775 | 87520876 |
SE_47398 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87536457 | 87536541 | 87531293 | 87531497 | 87539267 | 87539345 |
SE_47399 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87541356 | 87541464 | 87539267 | 87539345 | 87544128 | 87544275 |
(III) KB-C2-k.o.110α vs KB-C2 | ||||||||||||
AS ID | Gene ID | Gene name | Novel AS | Chr | Diff significant | P Value Junction Count Only | Exon Start (0 base) | Exon End | Upstream ES | Upstream EE | Downstream ES | Downstream EE |
SE_50129 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.1120059639 | 87605645 | 87605775 | 87601966 | 87603140 | 87713160 | 87715224 |
SE_50128 | ENSG00000085563 | ABCB1 | no | 7 | yes | 2.83848985472E-006 | 87605645 | 87605775 | 87600754 | 87601078 | 87713160 | 87715224 |
SE_50127 | ENSG00000085563 | ABCB1 | no | 7 | yes | 0 | 87602959 | 87603140 | 87600754 | 87601078 | 87713160 | 87713295 |
SE_50125 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.0641212769 | 87601272 | 87601371 | 87600754 | 87601078 | 87602959 | 87603140 |
SE_50123 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87595765 | 87595814 | 87585511 | 87585680 | 87600116 | 87600190 |
SE_50122 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87570171 | 87570223 | 87561262 | 87561387 | 87585511 | 87585680 |
SE_50121 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.0842138339 | 87566784 | 87566976 | 87566069 | 87566241 | 87570171 | 87570223 |
SE_50112 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87519325 | 87519466 | 87516508 | 87516665 | 87520775 | 87520876 |
SE_50116 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550170 | 87550296 | 87549850 | 87550054 | 87550467 | 87550578 |
SE_50117 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550724 | 87550838 | 87550467 | 87550578 | 87553760 | 87553932 |
SE_50114 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.5111213437 | 87541356 | 87541464 | 87539267 | 87539345 | 87544128 | 87544275 |
SE_50126 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.2905363226 | 87601966 | 87603140 | 87600754 | 87601078 | 87605645 | 87605775 |
SE_50124 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.2672547758 | 87601272 | 87601371 | 87600754 | 87601078 | 87601966 | 87603140 |
SE_50120 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.5376920457 | 87566784 | 87566976 | 87561262 | 87561387 | 87570171 | 87570223 |
SE_50113 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87536457 | 87536541 | 87531293 | 87531497 | 87539267 | 87539345 |
SE_50115 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87549347 | 87549518 | 87545862 | 87546024 | 87549850 | 87550054 |
SE_50118 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87566069 | 87566241 | 87561262 | 87561387 | 87566784 | 87566976 |
SE_50119 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.4481965282 | 87566069 | 87566241 | 87561262 | 87561387 | 87570171 | 87570223 |
(V) KB-C2-k.o.110β vs KB-C2 | ||||||||||||
AS ID | Gene ID | Gene name | Novel AS | Chr | Diff significant | P Value Junction Count Only | Exon Start (0 base) | Exon End | Upstream ES | Upstream EE | Downstream ES | Downstream EE |
SE_49198 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.4057523949 | 87601272 | 87601371 | 87600754 | 87601078 | 87601966 | 87603140 |
SE_49199 | ENSG00000085563 | ABCB1 | no | 7 | yes | 0.0006903622 | 87601272 | 87601371 | 87600754 | 87601078 | 87602959 | 87603140 |
SE_49190 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550170 | 87550296 | 87549850 | 87550054 | 87550467 | 87550578 |
SE_49191 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.365137306 | 87550467 | 87550578 | 87549850 | 87550054 | 87553760 | 87553932 |
SE_49192 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87550724 | 87550838 | 87550467 | 87550578 | 87553760 | 87553932 |
SE_49193 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87566069 | 87566241 | 87561262 | 87561387 | 87566784 | 87566976 |
SE_49194 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.448132556 | 87566069 | 87566241 | 87561262 | 87561387 | 87570171 | 87570223 |
SE_49195 | ENSG00000085563 | ABCB1 | yes | 7 | no | 0.5487589032 | 87566784 | 87566976 | 87561262 | 87561387 | 87570171 | 87570223 |
SE_49196 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.9285527169 | 87566784 | 87566976 | 87566069 | 87566241 | 87570171 | 87570223 |
SE_49197 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87595765 | 87595814 | 87585511 | 87585680 | 87600116 | 87600190 |
SE_49189 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87549347 | 87549518 | 87545862 | 87546024 | 87549850 | 87550054 |
SE_49188 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87541356 | 87541464 | 87539267 | 87539345 | 87544128 | 87544275 |
SE_49187 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87536457 | 87536541 | 87531293 | 87531497 | 87539267 | 87539345 |
SE_49186 | ENSG00000085563 | ABCB1 | yes | 7 | no | 1 | 87516508 | 87516665 | 87515227 | 87515428 | 87519325 | 87519466 |
SE_49200 | ENSG00000085563 | ABCB1 | no | 7 | yes | 1.1990408666E-014 | 87601272 | 87601371 | 87600754 | 87601078 | 87713160 | 87715224 |
SE_49201 | ENSG00000085563 | ABCB1 | yes | 7 | yes | 0.000649673 | 87601966 | 87603140 | 87600754 | 87601078 | 87605645 | 87605775 |
SE_49202 | ENSG00000085563 | ABCB1 | no | 7 | yes | 0 | 87602959 | 87603140 | 87600754 | 87601078 | 87713160 | 87713295 |
SE_49203 | ENSG00000085563 | ABCB1 | yes | 7 | yes | 0.0067345237 | 87602959 | 87603140 | 87601272 | 87601371 | 87713160 | 87713295 |
SE_49204 | ENSG00000085563 | ABCB1 | no | 7 | yes | 0 | 87605645 | 87605775 | 87600754 | 87601078 | 87713160 | 87715224 |
SE_49205 | ENSG00000085563 | ABCB1 | no | 7 | no | 0.0538934718 | 87605645 | 87605775 | 87601966 | 87603140 | 87713160 | 87715224 |
(I) KB-C2-k.o.cdk6 vs KB-C2 | |||||||||||
IJC KB-C2 | SJC KB-C2 | IJC KB-C2-k.o.cdk6 | SJC KB-C2-k.o.cdk6 | Inc Form Len | Skip Form Len | Average Inc Level1 (average PSI 1) | Average Inc Level2 (average PSI 2) | Increase Inclusion KB-C2 (ΔPSI>0) | Increase Exclusion KB-C2 (ΔPSI<0) | Increase Inclusion KB-C2-k.o.cdk6 (ΔPSI<0) | Increase Exclusion KB-C2-k.o.cdk6 (ΔPSI>0) |
7907 | 9 | 5933 | 0 | 298 | 149 | 0.998 | 1 | no | yes | yes | no |
2821 | 1 | 2975 | 0 | 232 | 149 | 0.999 | 1 | no | yes | yes | no |
12259 | 1 | 7047 | 0 | 295 | 149 | 1 | 1 | no_difference | no_difference | no_difference | no_difference |
11 | 35 | 38 | 129 | 298 | 149 | 0.136 | 0.128 | yes | no | no | yes |
0 | 2 | 50 | 1 | 298 | 149 | 0 | 0.962 | no | yes | yes | no |
2116 | 2 | 4377 | 3 | 262 | 149 | 0.998 | 0.999 | no | yes | yes | no |
2845 | 2 | 4885 | 4 | 274 | 149 | 0.999 | 0.998 | yes | no | no | yes |
3787 | 9 | 5847 | 1 | 298 | 149 | 0.995 | 1 | no | yes | yes | no |
2626 | 0 | 3200 | 14 | 256 | 149 | 1 | 0.993 | yes | no | no | yes |
1170 | 0 | 3565 | 27 | 197 | 149 | 1 | 0.99 | yes | no | no | yes |
349 | 1 | 931 | 0 | 197 | 149 | 0.996 | 1 | no | yes | yes | no |
1491 | 45 | 4298 | 83 | 298 | 149 | 0.943 | 0.963 | no | yes | yes | no |
857 | 0 | 1995 | 14 | 298 | 149 | 1 | 0.986 | yes | no | no | yes |
2 | 35 | 4 | 129 | 278 | 149 | 0.03 | 0.016 | yes | no | no | yes |
(II) KB-C2-k.o.cdk4 vs KB-C2 | |||||||||||
IJC KB-C2 | SJC KB-C2 | IJC KB-C2-k.o.cdk4 | SJC KB-C2-k.o.cdk4 | Inc Form Len | Skip Form Len | Average Inc Level1 (average PSI 1) | Average Inc Level2 (average PSI 2) | Increase Inclusion KB-C2 (ΔPSI>0) | Increase Exclusion KB-C2 (ΔPSI<0) | Increase Inclusion KB-C2-k.o.cdk4 (ΔPSI<0) | Increase Exclusion KB-C2-k.o.cdk4 (ΔPSI>0) |
3892 | 56 | 4300 | 83 | 341 | 149 | 0.968 | 0.958 | yes | no | no | yes |
2933 | 7 | 3565 | 27 | 198 | 149 | 0.997 | 0.99 | yes | no | no | yes |
54 | 0 | 50 | 1 | 1323 | 149 | 1 | 0.849 | yes | no | no | yes |
46 | 101 | 38 | 129 | 330 | 149 | 0.171 | 0.117 | yes | no | no | yes |
5497 | 14 | 5847 | 1 | 320 | 149 | 0.995 | 1 | no | yes | yes | no |
5076 | 4 | 4885 | 4 | 275 | 149 | 0.999 | 0.998 | yes | no | no | yes |
4228 | 0 | 4377 | 3 | 263 | 149 | 1 | 0.999 | yes | no | no | yes |
1914 | 1 | 1995 | 14 | 321 | 149 | 0.999 | 0.985 | yes | no | no | yes |
9 | 101 | 4 | 129 | 279 | 149 | 0.045 | 0.016 | yes | no | no | yes |
20 | 0 | 3 | 11 | 279 | 149 | 1 | 0.127 | yes | no | no | yes |
5188 | 1 | 5459 | 0 | 290 | 149 | 1 | 1 | no_difference | no_difference | no_difference | no_difference |
3032 | 4 | 2975 | 0 | 233 | 149 | 0.998 | 1 | no | yes | yes | no |
3431 | 0 | 3200 | 14 | 257 | 149 | 1 | 0.993 | yes | no | no | yes |
(III) KB-C2-k.o.110α vs KB-C2 | |||||||||||
IJC KB-C2 | SJC KB-C2 | IJC KB-C2-k.o.110α | SJC KB-C2-k.o.110α | Inc Form Len | Skip Form Len | Average Inc Level1 (average PSI 1) | Average Inc Level2 (average PSI 2) | Increase Inclusion KB-C2 (ΔPSI>0) | Increase Exclusion KB-C2 (ΔPSI<0) | Increase Inclusion KB-C2-k.o.110α (ΔPSI<0) | Increase Exclusion KB-C2-k.o.110α (ΔPSI>0) |
11 | 14 | 3 | 11 | 278 | 149 | 0.296 | 0.128 | yes | no | no | yes |
3 | 0 | 4 | 129 | 278 | 149 | 1 | 0.016 | yes | no | no | yes |
30 | 0 | 38 | 129 | 298 | 149 | 1 | 0.128 | yes | no | no | yes |
38 | 16 | 30 | 27 | 247 | 149 | 0.589 | 0.401 | yes | no | no | yes |
4622 | 7 | 3565 | 27 | 197 | 149 | 0.998 | 0.99 | yes | no | no | yes |
818 | 1 | 701 | 0 | 200 | 149 | 0.998 | 1 | no | yes | yes | no |
5347 | 145 | 4298 | 83 | 298 | 149 | 0.949 | 0.963 | no | yes | yes | no |
7533 | 7 | 5459 | 0 | 289 | 149 | 0.998 | 1 | no | yes | yes | no |
6308 | 5 | 4885 | 4 | 274 | 149 | 0.999 | 0.998 | yes | no | no | yes |
5327 | 2 | 4377 | 3 | 262 | 149 | 0.999 | 0.999 | no_difference | no_difference | no_difference | no_difference |
4489 | 32 | 3200 | 14 | 256 | 149 | 0.988 | 0.993 | no | yes | yes | no |
58 | 0 | 50 | 1 | 298 | 149 | 1 | 0.962 | yes | no | no | yes |
66 | 50 | 47 | 50 | 247 | 149 | 0.443 | 0.362 | yes | no | no | yes |
2856 | 2 | 2099 | 14 | 298 | 149 | 0.999 | 0.987 | yes | no | no | yes |
4051 | 26 | 2975 | 0 | 232 | 149 | 0.99 | 1 | no | yes | yes | no |
8098 | 9 | 5847 | 1 | 298 | 149 | 0.998 | 1 | no | yes | yes | no |
4749 | 1 | 4111 | 0 | 298 | 149 | 1 | 1 | no_difference | no_difference | no_difference | no_difference |
2402 | 2 | 1995 | 14 | 298 | 149 | 0.998 | 0.986 | yes | no | no | yes |
(V) KB-C2-k.o.110β vs KB-C2 | |||||||||||
IJC KB-C2 | SJC KB-C2 | IJC KB-C2-k.o.110β | SJC KB-C2-k.o.110β | Inc Form Len | Skip Form Len | Average Inc Level1 (average PSI 1) | Average Inc Level2 (average PSI 2) | Increase Inclusion KB-C2 (ΔPSI>0) | Increase Exclusion KB-C2 (ΔPSI<0) | Increase Inclusion KB-C2-k.o.110β (ΔPSI<0) | Increase Exclusion KB-C2-k.o.110β (ΔPSI>0) |
21 | 30 | 47 | 50 | 247 | 149 | 0.297 | 0.362 | no | yes | yes | no |
15 | 53 | 30 | 27 | 247 | 149 | 0.146 | 0.401 | no | yes | yes | no |
6090 | 5 | 4885 | 4 | 274 | 149 | 0.998 | 0.998 | no_difference | no_difference | no_difference | no_difference |
12 | 1 | 5 | 0 | 259 | 149 | 0.873 | 1 | no | yes | yes | no |
5428 | 7 | 4377 | 3 | 262 | 149 | 0.998 | 0.999 | no | yes | yes | no |
4885 | 1 | 4111 | 0 | 298 | 149 | 1 | 1 | no_difference | no_difference | no_difference | no_difference |
2345 | 0 | 1995 | 14 | 298 | 149 | 1 | 0.986 | yes | no | no | yes |
2793 | 0 | 2099 | 14 | 298 | 149 | 1 | 0.987 | yes | no | no | yes |
5439 | 107 | 4298 | 83 | 298 | 149 | 0.962 | 0.963 | no | yes | yes | no |
4078 | 0 | 3565 | 27 | 197 | 149 | 1 | 0.99 | yes | no | no | yes |
7421 | 5 | 5847 | 1 | 298 | 149 | 0.999 | 1 | no | yes | yes | no |
4110 | 0 | 3200 | 14 | 256 | 149 | 1 | 0.993 | yes | no | no | yes |
3805 | 9 | 2975 | 0 | 232 | 149 | 0.996 | 1 | no | yes | yes | no |
8034 | 1 | 5933 | 0 | 298 | 149 | 1 | 1 | no_difference | no_difference | no_difference | no_difference |
19 | 0 | 28 | 129 | 247 | 149 | 1 | 0.116 | yes | no | no | yes |
53 | 12 | 50 | 1 | 298 | 149 | 0.688 | 0.962 | no | yes | yes | no |
109 | 0 | 38 | 129 | 298 | 149 | 1 | 0.128 | yes | no | no | yes |
58 | 6 | 15 | 0 | 298 | 149 | 0.829 | 1 | no | yes | yes | no |
33 | 0 | 4 | 129 | 278 | 149 | 1 | 0.016 | yes | no | no | yes |
44 | 56 | 3 | 11 | 278 | 149 | 0.296 | 0.128 | yes | no | no | yes |