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		NCBI genome 108	0	Ensembl rel. 86	0
M.musculus	GRCm38		NCBI genome 106	0	Ensembl rel. 86	0
D.melanogaster	BDGP6		NCBI RefSeq rel.78	0	Ensembl rel. 86	0
C.elegans	WBcel235		NCBI RefSeq rel.78	0	Ensembl rel. 86	0
A.thaliana	TAIR 10		NCBI RefSeq rel.78	0	Ensembl Genome rel.32	0
O.sativa	IRGSP-1.0		NCBI RefSeq rel.71	0	Ensembl Genome rel.32	0

	version	total AS isoforms
Swiss-Prot	Release 2016/09	0

Database for annotaion
PDB	InterPro	KEGG	GEO
Oct. 3, 2016	Version 59.0	Dec. 17, 2016	GSE30611
PeptideAtlas
H.sapiens	M.musculus	D.melanogaster	C.elegans
Jan., 2016	Dec., 2014	Aug., 2012	Sep., 2013

H.sapiens
	No.	%
AS variant clusters	13380
AS variant clusters annotated with PDB data	7306	54.6 %
Unique AS regions	40434
Unique AS regions annotated with PDB data	17207	42.6 %

	N-ter.		middle		C-ter.		total
deletion	6430	15.9 %	9885	24.4 %	608	1.5 %	16923	41.9 %
insertion	550	1.4 %	2674	6.6 %	117	0.3 %	3341	8.3 %
substitution	3719	9.2 %	966	2.4 %	15485	38.3 %	20170	49.9 %
total	10699	26.5 %	13525	33.4 %	16210	40.1 %	40434	100.0 %

M.musculus
	No.	%
AS variant clusters	9589
AS variant clusters annotated with PDB data	4516	47.1 %
Unique AS regions	20208
Unique AS regions annotated with PDB data	7573	37.5 %

	N-ter.		middle		C-ter.		total
deletion	2535	12.5 %	5142	25.4 %	378	1.9 %	8055	39.9 %
insertion	471	2.3 %	1725	8.5 %	64	0.3 %	2260	11.2 %
substitution	1619	8.0 %	573	2.8 %	7701	38.1 %	9893	49.0 %
total	4625	22.9 %	7440	36.8 %	8143	40.3 %	20208	100.0 %

D.melanogaster
	No.	%
AS variant clusters	3482
AS variant clusters annotated with PDB data	1033	29.7 %
Unique AS regions	6697
Unique AS regions annotated with PDB data	1473	22.0 %

	N-ter.		middle		C-ter.		total
deletion	861	12.9 %	1967	29.4 %	141	2.1 %	2969	44.3 %
insertion	206	3.1 %	848	12.7 %	192	2.9 %	1246	18.6 %
substitution	882	13.2 %	258	3.9 %	1342	20.0 %	2482	37.1 %
total	1949	29.1 %	3073	45.9 %	1675	25.0 %	6697	100.0 %

C.elegans
	No.	%
AS variant clusters	4556
AS variant clusters annotated with PDB data	1250	27.4 %
Unique AS regions	7607
Unique AS regions annotated with PDB data	1720	22.6 %

	N-ter.		middle		C-ter.		total
deletion	2906	38.2 %	1570	20.6 %	36	0.5 %	4512	59.3 %
insertion	159	2.1 %	464	6.1 %	7	0.1 %	630	8.3 %
substitution	993	13.1 %	177	2.3 %	1295	17.0 %	2465	32.4 %
total	4058	53.3 %	2211	29.1 %	1338	17.6 %	7607	100.0 %

A.thaliana
	No.	%
AS variant clusters	4278
AS variant clusters annotated with PDB data	1703	39.8 %
Unique AS regions	5707
Unique AS regions annotated with PDB data	2105	36.9 %

	N-ter.		middle		C-ter.		total
deletion	697	12.2 %	1571	27.5 %	48	0.8 %	2316	40.6 %
insertion	132	2.3 %	817	14.3 %	20	0.4 %	969	17.0 %
substitution	492	8.6 %	288	5.0 %	1642	28.8 %	2422	42.4 %
total	1321	23.1 %	2676	46.9 %	1710	30.0 %	5707	100.0 %

O.sativa
	No.	%
AS variant clusters	5076
AS variant clusters annotated with PDB data	1819	35.8 %
Unique AS regions	6951
Unique AS regions annotated with PDB data	2188	31.5 %

	N-ter.		middle		C-ter.		total
deletion	419	6.0 %	692	10.0 %	53	0.8 %	1164	16.7 %
insertion	451	6.5 %	591	8.5 %	45	0.6 %	1087	15.6 %
substitution	719	10.3 %	1222	17.6 %	2759	39.7 %	4700	67.6 %
total	1589	22.9 %	2505	36.0 %	2857	41.1 %	6951	100.0 %

Swiss-Prot
	No.	%
AS variant clusters	20879
AS variant clusters annotated with PDB data	9280	44.4 %
Unique AS regions	38793
Unique AS regions annotated with PDB data	13915	35.9 %

	N-ter.		middle		C-ter.		total
deletion	5936	15.3 %	10916	28.1 %	1007	2.6 %	17859	46.0 %
insertion	688	1.8 %	2673	6.9 %	110	0.3 %	3471	8.9 %
substitution	4067	10.5 %	2458	6.3 %	10938	28.2 %	17463	45.0 %
total	10691	27.6 %	16047	41.4 %	12055	31.1 %	38793	100.0 %