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- (e.g. NM_000589, NM_002654, HIT000001802)
- (e.g. IL4, PKM2, LYPLA1)
- (e.g. 3565, 5315, 10434)
- (e.g. NM_010207, PX00698M05)
- (e.g. Fgfr2, Ctps2)
- (e.g. 14183, 55936)
- (e.g. MK09_MOUSE, PCLO_RAT)
- (e.g. Mapk9, pclo)

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Data source used in AS-ALPS

Transcript data for input
	NCBI Genome	NCBI RefSeq mRNA		FlcDNA *		total
	version	No. of data	version	No. of data	version	total
human	build36.3		Feb. 2009	0	H-InvDB 6.0	0
mouse	build37.1		Jan. 2008	0	FANTOM3	0

*: Dataset of Human FlcDNA includes sequences extracted from International Nucleotide Sequence Database.

	version	total AS isoforms
Swiss-Prot	Release 2010_12	0

Database for annotaion
PDB	InterPro	CAGE
Nov. 1, 2010	Version 23.0	March 27, 2009

Selected dataset

human
	No.	%
AS variant clusters	13134
AS variant clusters annotated with PDB data	5922	45.1 %
Unique AS regions	37789
Unique AS regions annotated with PDB data	11905	31.5 %

	N-ter.		middle		C-ter.		total
deletion	4697	12.4 %	8985	23.8 %	1778	4.7 %	15460	40.9 %
insertion	1112	2.9 %	2838	7.5 %	523	1.4 %	4473	11.8 %
substitution	3711	9.8 %	1074	2.8 %	13071	34.6 %	17856	47.3 %
total	9520	25.2 %	12897	34.1 %	15372	40.7 %	37789	100.0 %

mouse
	No.	%
AS variant clusters	8900
AS variant clusters annotated with PDB data	2966	33.3 %
Unique AS regions	16873
Unique AS regions annotated with PDB data	4101	24.3 %

	N-ter.		middle		C-ter.		total
deletion	3530	20.9 %	2916	17.3 %	1269	7.5 %	7715	45.7 %
insertion	1073	6.4 %	1291	7.7 %	1101	6.5 %	3465	20.5 %
substitution	1132	6.7 %	308	1.8 %	4253	25.2 %	5693	33.7 %
total	5735	34.0 %	4515	26.8 %	6623	39.3 %	16873	100.0 %

Swiss-Prot
	No.	%
AS variant clusters	9725
AS variant clusters annotated with PDB data	4090	42.1 %
Unique AS regions	17072
Unique AS regions annotated with PDB data	5711	33.5 %

	N-ter.		middle		C-ter.		total
deletion	2569	15.0 %	5301	31.1 %	472	2.8 %	8342	48.9 %
insertion	211	1.2 %	1016	6.0 %	42	0.2 %	1269	7.4 %
substitution	1707	10.0 %	1232	7.2 %	4522	26.5 %	7461	43.7 %
total	4487	26.3 %	7549	44.2 %	5036	29.5 %	17072	100.0 %

In human and mouse dataset, AS regions detected from incomplete CDS termius are excluded.
In Swiss-Prot dataset, AS regions with no experimental confirmation are excluded.

All dataset

human
	No.	%
AS variant clusters	15316
AS variant clusters annotated with PDB data	8036	52.5 %
Unique AS regions	74474
Unique AS regions annotated with PDB data	25933	34.8 %

	N-ter.		middle		C-ter.		total
deletion	24219	32.5 %	8985	12.1 %	8624	11.6 %	41828	56.2 %
insertion	1584	2.1 %	2838	3.8 %	547	0.7 %	4969	6.7 %
substitution	13007	17.5 %	1074	1.4 %	13596	18.3 %	27677	37.2 %
total	38810	52.1 %	12897	17.3 %	22767	30.6 %	74474	100.0 %

mouse
	No.	%
AS variant clusters	10427
AS variant clusters annotated with PDB data	4272	41.0 %
Unique AS regions	23897
Unique AS regions annotated with PDB data	6865	28.7 %

	N-ter.		middle		C-ter.		total
deletion	6734	28.2 %	2916	12.2 %	4200	17.6 %	13850	58.0 %
insertion	1283	5.4 %	1291	5.4 %	1128	4.7 %	3702	15.5 %
substitution	1566	6.6 %	308	1.3 %	4471	18.7 %	6345	26.6 %
total	9583	40.1 %	4515	18.9 %	9799	41.0 %	23897	100.0 %

Swiss-Prot
	No.	%
AS variant clusters	12648
AS variant clusters annotated with PDB data	5819	46.0 %
Unique AS regions	21517
Unique AS regions annotated with PDB data	8322	38.7 %

	N-ter.		middle		C-ter.		total
deletion	2569	11.9 %	8256	38.4 %	472	2.2 %	11297	52.5 %
insertion	211	1.0 %	1834	8.5 %	42	0.2 %	2087	9.7 %
substitution	1707	7.9 %	1904	8.8 %	4522	21.0 %	8133	37.8 %
total	4487	20.9 %	11994	55.7 %	5036	23.4 %	21517	100.0 %