Data source used in AS-ALPS

Transcript data for input

	Genome	NCBI RefSeq mRNA		other transcript data		total
	version	No. of data	version	No. of data	data source
H.sapiens	Ensembl rel. 62		rel. 47	0	Ensembl rel. 62	0
M.musculus	Ensembl rel. 62		rel. 47	0	Ensembl rel. 62	0
D.melanogaster	Ensembl rel. 62		rel. 45	0	Ensembl rel. 62	0
C.elegans	Ensembl rel. 62		rel. 45	0	Ensembl rel. 62	0
A.thaliana	TAIR 10		rel. 47	0	TAIR 10	0
O.sativa	TIGR 6.1		rel. 47	0	TIGR 6.1	0

	version	total AS isoforms
Swiss-Prot	Release 2012_06	0

Database for annotaion

PDB	InterPro	KEGG
May. 7, 2012	Version 32.0	Aug. 26, 2011

H.sapiens

	No.	%
AS variant clusters	12924
AS variant clusters annotated with PDB data	6437	49.8 %
Unique AS regions	39837
Unique AS regions annotated with PDB data	14686	36.9 %

	N-ter.		middle		C-ter.		total
deletion	6921	17.4 %	10189	25.6 %	475	1.2 %	17585	44.1 %
insertion	648	1.6 %	2657	6.7 %	83	0.2 %	3388	8.5 %
substitution	3880	9.7 %	1558	3.9 %	13426	33.7 %	18864	47.4 %
total	11449	28.7 %	14404	36.2 %	13984	35.1 %	39837	100.0 %

M.musculus

	No.	%
AS variant clusters	9488
AS variant clusters annotated with PDB data	3999	42.1 %
Unique AS regions	20140
Unique AS regions annotated with PDB data	6541	32.5 %

	N-ter.		middle		C-ter.		total
deletion	2923	14.5 %	5064	25.1 %	218	1.1 %	8205	40.7 %
insertion	431	2.1 %	1801	8.9 %	37	0.2 %	2269	11.3 %
substitution	1727	8.6 %	1090	5.4 %	6849	34.0 %	9666	48.0 %
total	5081	25.2 %	7955	39.5 %	7104	35.3 %	20140	100.0 %

D.melanogaster

	No.	%
AS variant clusters	2569
AS variant clusters annotated with PDB data	731	28.5 %
Unique AS regions	4194
Unique AS regions annotated with PDB data	974	23.2 %

	N-ter.		middle		C-ter.		total
deletion	802	19.1 %	781	18.6 %	20	0.5 %	1603	38.2 %
insertion	171	4.1 %	457	10.9 %	5	0.1 %	633	15.1 %
substitution	737	17.6 %	177	4.2 %	1044	24.9 %	1958	46.7 %
total	1710	40.8 %	1415	33.7 %	1069	25.5 %	4194	100.0 %

C.elegans

	No.	%
AS variant clusters	4026
AS variant clusters annotated with PDB data	861	21.4 %
Unique AS regions	6252
Unique AS regions annotated with PDB data	1093	17.5 %

	N-ter.		middle		C-ter.		total
deletion	1357	21.7 %	1064	17.0 %	37	0.6 %	2458	39.3 %
insertion	431	6.9 %	728	11.6 %	35	0.6 %	1194	19.1 %
substitution	854	13.7 %	325	5.2 %	1421	22.7 %	2600	41.6 %
total	2642	42.3 %	2117	33.9 %	1493	23.9 %	6252	100.0 %

A.thaliana

	No.	%
AS variant clusters	4745
AS variant clusters annotated with PDB data	1593	33.6 %
Unique AS regions	6482
Unique AS regions annotated with PDB data	1964	30.3 %

	N-ter.		middle		C-ter.		total
deletion	692	10.7 %	1589	24.5 %	51	0.8 %	2332	36.0 %
insertion	253	3.9 %	1183	18.3 %	21	0.3 %	1457	22.5 %
substitution	546	8.4 %	375	5.8 %	1772	27.3 %	2693	41.5 %
total	1491	23.0 %	3147	48.5 %	1844	28.4 %	6482	100.0 %

O.sativa

	No.	%
AS variant clusters	8406
AS variant clusters annotated with PDB data	2399	28.5 %
Unique AS regions	12488
Unique AS regions annotated with PDB data	3169	25.4 %

	N-ter.		middle		C-ter.		total
deletion	1145	9.2 %	1319	10.6 %	93	0.7 %	2557	20.5 %
insertion	1210	9.7 %	1472	11.8 %	68	0.5 %	2750	22.0 %
substitution	1658	13.3 %	427	3.4 %	5096	40.8 %	7181	57.5 %
total	4013	32.1 %	3218	25.8 %	5257	42.1 %	12488	100.0 %

Swiss-Prot

	No.	%
AS variant clusters	14397
AS variant clusters annotated with PDB data	6950	48.3 %
Unique AS regions	24629
Unique AS regions annotated with PDB data	10027	40.7 %

	N-ter.		middle		C-ter.		total
deletion	3055	12.4 %	9171	37.2 %	514	2.1 %	12740	51.7 %
insertion	298	1.2 %	2145	8.7 %	54	0.2 %	2497	10.1 %
substitution	2039	8.3 %	2052	8.3 %	5301	21.5 %	9392	38.1 %
total	5392	21.9 %	13368	54.3 %	5869	23.8 %	24629	100.0 %