Statistics in AS-ALPS

Transcript data for input

	NCBI Genome	NCBI RefSeq mRNA		FlcDNA		total
	version	No. of data	version	No. of data	version
human	build 36.1	24,655	Jul. 2007	173,690 *	H-InvDB4	198,345
mouse	build 37.1	20,917	Jan. 2008	56,722	FANTOM3	77,639

*:Human mRNAs extracted from International Nucleotide Sequence Database were included.

3D structure data for annotaion

PDB	Superfamily
July 31, 2007	Version 1.69

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Detected AS regions in human

All data

(including probably artifactual AS regions)

	No.	%
AS variant clusters	14,555
AS variant clusters annotated with PDB data	6,898	47.4
Unique AS regions	62,257
Unique AS regions annotated with PDB data	19,862	31.9

	N-ter.		middle		C-ter.		total
deletion	22,169	35.6%	6,801	10.9%	6,420	10.3%	35,390	56.8%
insertion	2,020	3.2%	2,206	3.5%	424	0.7%	4,650	7.5%
substitution	10,157	16.3%	935	1.5%	11,125	17.9%	22,217	35.7%
total	34,346	55.2%	9,942	16.0%	17,969	28.9%	62,257	100.0%

Selected data

in which probably artifactual AS regions:
        1) AS regions detected from incomplete CDS terminus
        2) AS regions whose length was less than three
were excluded.

	No.	%
AS variant clusters	11,926
AS variant clusters annotated with PDB data	5,067	42.5
Unique AS regions	31,928
Unique AS regions annotated with PDB data	10,056	31.5

	N-ter.		middle		C-ter.		total
deletion	6,453	20.2%	6,172	19.3%	1,344	4.2%	13,969	43.8%
insertion	1,071	3.4%	1,818	5.7%	251	0.8%	3,140	9.8%
substitution	3,495	10.9%	804	2.5%	10,520	32.9%	14,819	46.4%
total	11,019	34.5%	8,794	27.5%	12,115	37.9%	31,928	100.0%

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Detected AS regions in mouse

All data

(including probably artifactual AS regions)

	No.	%
AS variant clusters	9,783
AS variant clusters annotated with PDB data	3,761	38.4
Unique AS regions	22,086
Unique AS regions annotated with PDB data	6,023	27.3

	N-ter.		middle		C-ter.		total
deletion	6,293	28.5%	2,838	12.8%	3,783	17.1%	12,914	58.5%
insertion	893	4.0%	1,202	5.4%	591	2.7%	2,686	12.2%
substitution	1,654	7.5%	328	1.5%	4,504	20.4%	6,486	29.4%
total	8,840	40.0%	4,368	19.8%	8,878	40.2%	22,086	100.0%

Selected data

in which probably artifactual AS regions:
        1) AS regions detected from incomplete CDS terminus
        2) AS regions whose length was less than three
were excluded.

	No.	%
AS variant clusters	7,666
AS variant clusters annotated with PDB data	2,675	34.9
Unique AS regions	13,893
Unique AS regions annotated with PDB data	3,676	26.5

	N-ter.		middle		C-ter.		total
deletion	3,149	22.7%	2,440	17.6%	830	6.0%	6,419	46.2%
insertion	567	4.1%	945	6.8%	454	3.3%	1,966	14.2%
substitution	1,099	7.9%	272	2.0%	4,137	29.8%	5,508	39.6%
total	4,815	34.7%	3,657	26.3%	5,421	39.0%	13,893	100.0%