Statistics

Representative AS variant (RASV) information about the number, position category, pattern, influence to protein function and conservation with mouse in H-Inv full-length cDNA datast is presented here. RASV information about the number, position catagory pattern and influence to protein function in H-Inv all transcript dataset and that about the number, position category and pattern in Mouse full-length cDNA datase are also presented respectively. Information of splice-site sequence and NAGNAG motif is shown as supplementary in three datasets.

Basic summary of RASVs in three datasets

	H-Inv full-length cDNA	H-Inv all transcript	Mouse full-length cDNA
Average number of RASVs in AS locus	2.7	3.6	2.9
Average number of AS exons in RASV	2.4	3.2	2.2
Percentage of GT-AG in all splice-site sequences	97.6%	98.4%	99%

Go to H-Inv full-length cDNAs
Go to H-Inv all transcripts
Go to Mouse full-length cDNAs

i) H-Inv full-length cDNAs

Table 1. Number and position category of RASVs

	#Locus	#cDNA	#Total exon	#Alternative exon	#Constitutive exon
Representative AS Variants (RASVs)	7801	20803	207399	50399	157000
5'-end	5141	14252	20803	8889	11914
Internal	6868	18400	165793	35162	130631
3'-end	3212	8945	20803	6348	14455
5'UTR*	4021	7259	11867	4572	7295
CDS*	7525	15752	144984	31549	113435
3'UTR*	1815	2385	5346	1768	3578

*They were analyzed by using RASVs whose ORF were identified as full-length.

Table 2. AS pattern of RASVs

		#Locus	#cDNA
Cassette (Skipped exon) [including multiple cassette]		3677	9821
Internal acceptor (Alternative 3' splice)		2269	6170
Internal donor (Alternative 5' splice)		2274	5992
Mutually exclusive		251	608
Retained intron		2287	6180
Alternative first	5'-end	2495	6700
Alternative first acceptor	5'-end	2524	7122
Alternative last	3'-end	952	2512
Alternative last donor	3'-end	1303	3470

Table 3. Numbers in which RASVs influence the possible protein functions

	#Locus	#cDNA
AS affecting protein function total	3256	8237
Ptotein motif	2501	6303
GO term	896	2444
Subcelluler localization signal	2054	5435
Transmembrane domain	443	1101
Cpmplex AS pattern total	844	2262
Bridged*	71	298
Nested**	771	1972
Multiple CDS***	37	79

*Two AS variants were arrayed tandemly without sharing any exons and another transcript 'bridged' them, sharing at least some of its exons with both of them and also sharing the same reading frame to their ORFs.
**CDS region of one AS variant was not shared with another variant.
***Different ORFs >200 bp in length were annotated independently for different AS variants sharing at least some of the exons but not sharing any reading frame.

Table 4. Genomic conservation of RASVs in humans and mice

	Total	Non-conserved*	Genome-conserved*	Transcript-conserved*	Equally spliced variant (ESV)*	Conserved AS*
All exons	207399	27567	22396	157436	-	-
AS exons	50399	11994	8757	29648	-	-
AS variants	20803	8459	4469	2381	4995	499
AS loci	7801	1686	1258	815	3817	225

*See Genomic comparison between RASVs and mouse cDNAs.

Table 5. Relationship between conservation and splicing in RASV exons

	Total	CDS	Protein motif	Retrotransposon	ESE
C/CS exons*	141427	94751	25504	2686	137390
C/AS exons*	38405	19383	5055	2268	36486
NC/CS exons*	15573	6713	1737	2538	14894
NC/AS exons*	11994	3184	669	4540	11555
All exons	207399	124031	32965	12032	200325

*C: Conserved, NC: Non-conserved, CS: Constitutively spliced, AS: Alternatively spliced

Supplementary Table 1. Splice-site sequence of RASVs

Total	GT - AG	GC - AG	AT - AC	Others
186596	182163	1164	173	3096

Supplementary Table 2. NAGNAG motif of RASVs

Motif	Observed	E type	I type	E+I type
AAGAAG	64	50	16	2
AAGCAG	216	56	160	0
AAGGAG	274	266	8	0
AAGTAG	28	7	21	0
CAGAAG	1070	1039	31	0
CAGCAG	1003	645	366	8
CAGGAG	3497	3454	43	0
CAGTAG	106	77	29	0
GAGAAG	32	10	22	0
GAGCAG	284	8	276	0
GAGGAG	35	18	19	2
GAGTAG	68	5	63	0
TAGAAG	445	424	21	0
TAGCAG	291	202	89	0
TAGGAG	1532	1518	14	0
TAGTAG	88	65	23	0

ii) H-Inv all transcripts

Table 1. Number and position category of RASVs

	#Locus	#Transcript	#Total exon	#Alternative exon	#Constitutive exon
Representative AS Variants (RASVs)	13704	49308	478479	156581	321898
5'-end	8997	34416	49308	22560	26748
Internal	12459	45468	379863	114181	265682
3'-end	7499	29050	49308	19840	29468
5'UTR*	7346	17010	28410	13108	15302
CDS*	13286	37275	334147	100583	233564
3'UTR*	4139	6303	14532	5846	8686

*They were analyzed by using RASVs whose ORF was identified as full-length.

Table 2. AS patterns of RASVs

		#Locus	#Transcript
Cassette (Skipped exon) [including multiple cassette]		7970	30048
Internal acceptor (Alternative 3' splice)		4944	18376
Internal donor (Alternative 5' splice)		5150	18616
Mutually exclusive		915	2968
Retained intron		4303	15033
Alternative first	5'-end	5046	18581
Alternative first acceptor	5'-end	4487	16798
Alternative last	3'-end	3009	10920
Alternative last donor	3'-end	3844	13926

Table 3. Numbers in which RASVs influence the possible protein functions

	#Locus	#Transcript
AS affecting protein function total	7215	22891
Protein motif	5858	19286
GO term	2432	7451
Subcelluler localization signal	4669	13550
Transmembrane domain	1179	4124
Cpmplex AS pattern total	2572	9427
Bridged*	509	2678
Nested**	2280	7484
Multiple CDS**	127	332

*Two AS variants were arrayed tandemly without sharing any exons and another transcript 'bridged' them, sharing at least some of its exons with both of them and also sharing the same reading frame to their ORFs.
**CDS region of one AS variant was not shared with another variant.
***Different ORFs >200 bp in length were annotated independently for different AS variants sharing at least some of the exons but not sharing any reading frame.

Supplementary Table 1. Splice site sequence of RASVs

Total	GT - AG	GC - AG	AT - AC	Others
1977773	1946428	8080	1525	21740

Supplementary Table 2. NAGNAG motif of RASVs

Motif	Observed	E type	I type	E+I type
AAGAAG	463	399	78	14
AAGCAG	1611	450	1164	0
AAGGAG	2020	1985	35	0
AAGTAG	310	85	225	0
CAGAAG	8871	8615	256	0
CAGCAG	7413	4905	2591	83
CAGGAG	27188	26912	276	0
CAGTAG	993	730	263	0
GAGAAG	153	34	119	0
GAGCAG	2131	60	2071	0
GAGGAG	262	160	111	9
GAGTAG	394	24	370	0
TAGAAG	3478	3362	116	0
TAGCAG	2406	1699	707	0
TAGGAG	12317	12239	78	0
TAGTAG	577	434	143	0

iii) Mouse full-length cDNAs

Table 1. Number and position category of RASVs

	#Locus	#cDNA	#Total exon	#Alternative exon	#Constitutive exon
Representative AS Variants (RASVs)	10237	29955	272441	65664	206777
5'-end	5306	16137	29955	10228	19727
Internal	8728	25661	212531	43291	169240
3'-end	6436	19997	29955	12145	17810

Table 2. AS pattern of RASVs

		#Locus	#cDNA
Cassette (Skipped exon) [including multiple cassette]		3707	11183
Internal acceptor (Alternative 3' splice)		2041	5797
Internal donor (Alternative 5' splice)		2225	6357
Mutually exclusive		193	561
Retained intron		2716	7615
Alternative first	5'-end	2861	8757
Alternative first acceptor	5'-end	1934	5529
Alternative last	3'-end	2265	6847
Alternative last donor	3'-end	4420	13765

Supplementary Table 1. Splice site sequence of RASVs

Total	GT - AG	GC - AG	AT - AC	Others
242486	241133	88	126	1139

Supplementary Table 2. NAGNAG motif of RASVs

Motif	Observed	E type	I type	E+I type
AAGAAG	131	108	26	3
AAGCAG	300	91	209	0
AAGGAG	319	309	10	0
AAGTAG	77	24	53	0
CAGAAG	1879	1801	78	0
CAGCAG	1605	1059	568	22
CAGGAG	5160	5113	47	0
CAGTAG	237	181	56	0
GAGAAG	40	12	28	0
GAGCAG	424	17	407	0
GAGGAG	35	24	12	1
GAGTAG	68	1	67	0
TAGAAG	708	671	37	0
TAGCAG	580	382	198	0
TAGGAG	2402	2378	24	0
TAGTAG	108	86	22	0