Table 3.

Identification of alternative splicing events using rMATS (replicate Multivariate Analysis of Transcript Splicing)²⁷.

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.