Table 3.
AS Events Summary | E15 vs E18 | E15 vs P0 | E15 vs P3 | E15 vs P6 | E15 vs P9 | E18 vs P0 | E18 vs P3 | E18 vs P6 | E18 vs P9 | P0 vs P3 | P0 vs P6 | P0 vs P9 | P3 vs P6 | P3 vs P9 | P6 vs P9 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SE | 7 | 52 | 40 | 55 | 55 | 120 | 75 | 123 | 87 | 10 | 9 | 14 | 3 | 5 | 0 |
MXE | 3 | 6 | 18 | 8 | 12 | 6 | 16 | 4 | 10 | 14 | 2 | 3 | 10 | 14 | 0 |
RI | 62 | 46 | 25 | 26 | 37 | 73 | 29 | 31 | 34 | 6 | 2 | 9 | 0 | 1 | 2 |
A5SS | 1 | 9 | 0 | 4 | 0 | 7 | 0 | 2 | 0 | 1 | 1 | 2 | 0 | 0 | 0 |
A3SS | 3 | 4 | 3 | 3 | 3 | 12 | 5 | 7 | 5 | 1 | 2 | 0 | 1 | 0 | 1 |
Exon Skipping Events | |||||||||||||||
Exon ID | Coordinates (mm10) | strand | Transcript ID | Gene Name | E15 | E18 | P0 | P3 | P6 | P9 | |||||
ENSMUSE00000334942 | 19:57051130-57051234 | − | ENSMUST00000111559 | Ablim1 | NA | 0.13 | 0.61 | 0.729 | 0.66 | 0.612 | |||||
ENSMUSE00000668725 | 3:148849766-148849804 | − | ENSMUST00000197567 | Adgrl2 | 0.202 | 0.24 | 0.61 | NA | 0.57 | 0.611 | |||||
ENSMUSE00001324776 | 1:82891460-82891507 | + | ENSMUST00000190052 | Agfg1 | 0.232 | 0.18 | 0.41 | 0.532 | 0.48 | 0.489 | |||||
ENSMUSE00001039657 | 18:6057517-6057591 | − | ENSMUST00000182066 | Arhgap12 | 0.289 | 0.32 | 0.82 | NA | NA | NA | |||||
ENSMUSE00000700987 | 2:10056770-10056806 | − | ENSMUST00000114897 | Atp5c1 | 0.822 | 0.76 | 0.55 | 0.55 | 0.62 | 0.574 | |||||
ENSMUSE00000230008 | 18:32426224-32426352 | + | ENSMUST00000091967 | Bin1 | NA | 0.68 | 0.18 | NA | NA | NA | |||||
ENSMUSE00000217920 | 9:70004306-70004341 | + | ENSMUST00000034754 | Bnip2 | NA | 0.5 | 0.9 | 0.806 | NA | 0.845 | |||||
ENSMUSE00000736151 | 10:127064202-127064453 | + | ENSMUST00000133115 | Cdk4 | 0.959 | 0.96 | 0.8 | NA | NA | NA | |||||
ENSMUSE00000691476 | 5:112251747-112251797 | − | ENSMUST00000112385 | Cryba4 | 0.974 | 0.98 | NA | 0.994 | 0.99 | 0.99 | |||||
ENSMUSE00000311733 | 14:47726471-47726554 | + | ENSMUST00000022391 | Ktn1 | NA | 0.24 | 0.5 | 0.476 | NA | 0.517 | |||||
ENSMUSE00000440236 | 6:93680789-93680877 | − | ENSMUST00000204347 | Magi1 | 0.118 | 0.09 | NA | NA | 0.48 | 0.655 | |||||
ENSMUSE00000667965 | 7:143518850-143518885 | − | ENSMUST00000072727 | Nap1l4 | 0.477 | 0.42 | 0.29 | 0.228 | 0.25 | 0.245 | |||||
ENSMUSE00001311933 | 2:105695306-105695456 | + | ENSMUST00000111082 | Pax6 | 0.995 | 1 | 0.94 | 0.993 | 1 | NA | |||||
ENSMUSE00000317905 | 15:93452117-93452173 | + | ENSMUST00000068457 | Pphln1 | 0.151 | 0.07 | 0.57 | 0.356 | 0.5 | 0.639 | |||||
ENSMUSE00000635082 | 9:86790056-86790139 | − | ENSMUST00000074468 | Snap91 | NA | 0.85 | 0.27 | 0.248 | 0.2 | NA | |||||
ENSMUSE00001196118 | 11:80393084-80393176 | + | ENSMUST00000123726 | Zfp207 | 0.368 | NA | 0.67 | NA | 0.61 | 0.593 | |||||
Intron Retention Events | |||||||||||||||
Exon ID | Coordinates (mm10) | strand | Transcript ID | Gene Name | E15 | E18 | P0 | P3 | P6 | P9 | |||||
ENSMUSE00000784872 | 3:103174340-103177419 | + | ENSMUST00000136937 | Bcas2 | 0.039 | 0.0685 | 0.026 | 0.035 | 0.0225 | 0.031 | |||||
ENSMUSE00000787504 | 11:101295534-101296316 | − | ENSMUST00000139997 | Becn1 | NA | 0.1185 | 0.0635 | 0.062 | 0.051 | 0.044 | |||||
ENSMUSE00000643467 | 2:91013238-91019497 | + | ENSMUST00000111452 | Celf1 | 0.3755 | 0.709 | 0.612 | 0.8395 | 0.8565 | 0.846 | |||||
ENSMUSE00001342001 | 1:165338188-165340023 | − | ENSMUST00000193353 | Dcaf6 | 0.082 | 0.1555 | 0.0585 | 0.0635 | 0.052 | 0.0535 | |||||
ENSMUSE00000842895 | 11:106782469-106784018 | − | ENSMUST00000133426 | Ddx5 | 0.1375 | 0.1835 | 0.2265 | 0.3185 | 0.302 | 0.3625 | |||||
ENSMUSE00000492954 | 3:95628541-95632102 | + | ENSMUST00000037983 | Ensa | 0.458 | 0.6615 | 0.4515 | 0.4335 | 0.4195 | NA | |||||
ENSMUSE00001357022 | 3:152213977-152215630 | + | ENSMUST00000196062 | Fubp1 | 0.0095 | 0.0535 | 0.058 | 0.0585 | 0.032 | 0.0515 | |||||
ENSMUSE00000857219 | 1:161038225-161038539 | + | ENSMUST00000160516 | Gas5 | 0.2265 | 0.289 | 0.0485 | 0.068 | 0.1195 | 0.099 | |||||
ENSMUSE00001326780 | 7:31134414-31135739 | − | ENSMUST00000188032 | Gramd1a | 0.4465 | 0.7265 | 0.28 | 0.4175 | 0.319 | 0.307 | |||||
ENSMUSE00000765273 | 11:50379468-50379964 | + | ENSMUST00000134230 | Hnrnph1 | 0.093 | NA | 0.2775 | 0.1575 | 0.181 | 0.165 | |||||
ENSMUSE00000756514 | X:95947770-95950446 | − | ENSMUST00000126605 | Las1l | 0.0135 | 0.034 | 0.0545 | 0.041 | 0.043 | 0.0575 | |||||
ENSMUSE00000764755 | X:94537676-94538065 | − | ENSMUST00000153386 | Maged1 | 0.064 | 0.1 | 0.0455 | 0.0525 | 0.045 | 0.0545 | |||||
ENSMUSE00000777868 | 5:21743379-21746090 | + | ENSMUST00000125693 | Pmpcb | 0.0105 | 0.026 | 0.0865 | 0.033 | 0.0485 | 0.0665 | |||||
ENSMUSE00000740654 | X:8143848-8144679 | − | ENSMUST00000141925 | Rbm3 | 0.0675 | 0.0985 | 0.0195 | 0.0405 | 0.044 | 0.0695 | |||||
ENSMUSE00001332031 | 1:55014483-55016490 | − | ENSMUST00000187500 | Sf3b1 | 0.1365 | 0.178 | 0.2265 | 0.264 | 0.284 | 0.282 |
Summary of the number of high confident Alternative Splicing (AS) events detected using rMATS pipeline (FDR <0.01) across developmental stages with replicates. Selected high confident exon skipping and intron retention events detected using rMATS pipeline (FDR <0.01) across developmental stages with replicates. Values across stages correspond to PSI values of the exons. Abbreviations used in the table stand for the following types of splicing events and definitions: SE- Skipped Exon, MXE- Mutually Exclusive Exon, RI- Retained Intron, A5SS- Alternative 5′ Splice Site, A3SS- Alternative 3′ Splice Site, PSI- Percent Spliced Index, FDR- False Discovery Rate.