Data source used in AS-ALPS

Input data
	Genome	NCBI RefSeq mRNA		other transcript data		total
	version	No. of data	version	No. of data	data source	total
H.sapiens	GRCh38	43099	NCBI genome 108	95656	Ensembl rel. 90	138755
M.musculus	GRCm38	29914	NCBI genome 106	62935	Ensembl rel. 90	92849
D.melanogaster	BDGP6	30469	NCBI RefSeq rel.84	30356	Ensembl rel. 90	60825
C.elegans	WBcel235	28221	NCBI RefSeq rel.84	31562	Ensembl rel. 90	59783
A.thaliana	TAIR 10	48148	NCBI RefSeq rel.84	48321	Ensembl Genome rel.37	96469
O.sativa	IRGSP-1.0	40907	NCBI RefSeq rel.84	42132	Ensembl Genome rel.37	83039

	version	total AS isoforms
Swiss-Prot	Release 2017/10	60065

Database for annotaion
PDB	InterPro	KEGG	GEO
Oct. 2, 2017	Version 59.0	Nov. 17, 2017	GSE30611
PeptideAtlas
H.sapiens	M.musculus	D.melanogaster	C.elegans
Dec., 2016	Jan., 2016	Aug., 2012	Sep., 2013

H.sapiens
	No.	%
AS variant clusters	13396
AS variant clusters annotated with PDB data	7473	55.8 %
Unique AS regions	40709
Unique AS regions annotated with PDB data	17792	43.7 %

	N-ter.		middle		C-ter.		total
deletion	6437	15.8 %	9958	24.5 %	614	1.5 %	17009	41.8 %
insertion	561	1.4 %	2689	6.6 %	119	0.3 %	3369	8.3 %
substitution	3725	9.2 %	975	2.4 %	15631	38.4 %	20331	49.9 %
total	10723	26.3 %	13622	33.5 %	16364	40.2 %	40709	100.0 %

M.musculus
	No.	%
AS variant clusters	10117
AS variant clusters annotated with PDB data	5025	49.7 %
Unique AS regions	21468
Unique AS regions annotated with PDB data	8545	39.8 %

	N-ter.		middle		C-ter.		total
deletion	2668	12.4 %	5354	24.9 %	403	1.9 %	8425	39.2 %
insertion	496	2.3 %	1831	8.5 %	66	0.3 %	2393	11.1 %
substitution	1700	7.9 %	582	2.7 %	8368	39.0 %	10650	49.6 %
total	4864	22.7 %	7767	36.2 %	8837	41.2 %	21468	100.0 %

D.melanogaster
	No.	%
AS variant clusters	3489
AS variant clusters annotated with PDB data	1060	30.4 %
Unique AS regions	6716
Unique AS regions annotated with PDB data	1524	22.7 %

	N-ter.		middle		C-ter.		total
deletion	869	12.9 %	1975	29.4 %	145	2.2 %	2989	44.5 %
insertion	203	3.0 %	851	12.7 %	186	2.8 %	1240	18.5 %
substitution	886	13.2 %	257	3.8 %	1344	20.0 %	2487	37.0 %
total	1958	29.2 %	3083	45.9 %	1675	24.9 %	6716	100.0 %

C.elegans
	No.	%
AS variant clusters	4645
AS variant clusters annotated with PDB data	1293	27.8 %
Unique AS regions	7829
Unique AS regions annotated with PDB data	1781	22.7 %

	N-ter.		middle		C-ter.		total
deletion	2970	37.9 %	1596	20.4 %	36	0.5 %	4602	58.8 %
insertion	188	2.4 %	497	6.3 %	7	0.1 %	692	8.8 %
substitution	1016	13.0 %	166	2.1 %	1353	17.3 %	2535	32.4 %
total	4174	53.3 %	2259	28.9 %	1396	17.8 %	7829	100.0 %

A.thaliana
	No.	%
AS variant clusters	8048
AS variant clusters annotated with PDB data	3286	40.8 %
Unique AS regions	12477
Unique AS regions annotated with PDB data	4575	36.7 %

	N-ter.		middle		C-ter.		total
deletion	2320	18.6 %	2222	17.8 %	87	0.7 %	4629	37.1 %
insertion	398	3.2 %	1319	10.6 %	38	0.3 %	1755	14.1 %
substitution	1313	10.5 %	371	3.0 %	4409	35.3 %	6093	48.8 %
total	4031	32.3 %	3912	31.4 %	4534	36.3 %	12477	100.0 %

O.sativa
	No.	%
AS variant clusters	6222
AS variant clusters annotated with PDB data	2506	40.3 %
Unique AS regions	8290
Unique AS regions annotated with PDB data	3004	36.2 %

	N-ter.		middle		C-ter.		total
deletion	1109	13.4 %	1098	13.2 %	134	1.6 %	2341	28.2 %
insertion	352	4.2 %	372	4.5 %	29	0.3 %	753	9.1 %
substitution	651	7.9 %	1131	13.6 %	3414	41.2 %	5196	62.7 %
total	2112	25.5 %	2601	31.4 %	3577	43.1 %	8290	100.0 %

Swiss-Prot
	No.	%
AS variant clusters	21160
AS variant clusters annotated with PDB data	9842	46.5 %
Unique AS regions	39192
Unique AS regions annotated with PDB data	14869	37.9 %

	N-ter.		middle		C-ter.		total
deletion	5995	15.3 %	11025	28.1 %	1015	2.6 %	18035	46.0 %
insertion	696	1.8 %	2702	6.9 %	111	0.3 %	3509	9.0 %
substitution	4125	10.5 %	2483	6.3 %	11040	28.2 %	17648	45.0 %
total	10816	27.6 %	16210	41.4 %	12166	31.0 %	39192	100.0 %