Cross-kingdom patterns of alternative splicing and splice recognition

McGuire, Abigail M; Pearson, Matthew D; Neafsey, Daniel E; Galagan, James E

doi:10.1186/gb-2008-9-3-r50

Table 4 Intron and exon lengths for controls and splice variants

From: Cross-kingdom patterns of alternative splicing and splice recognition

	Kingdom	Intron density*	Genome assembly size (Mb)^†	Average intron length^‡	Average RI length^§¶	Average intron length next to CE^¥	No. of CEs with unambiguous boundaries^#	% introns >200 bp**	Average exon length^¶††	Average internal exon length^¶‡‡	Average CE length^§§
D. rerio	Animal	7.2	1,547	2,940	130	3,485	903	71%	180	132	113
T. rubripes	Animal	8.1	393	582	126	641	22	45%	140	119	103
B. floridae	Animal	5.7	923	1,283	115	1,424	135	91%	151	124	111
C. savignyi	Animal	9.1	164	710	87	595	20	82%	148	130	123
C. intestinalis	Animal	7.4	117	457	152	544	327	76%	181	143	122
N. vectensis	Animal	4.1	357	823	167	820	26	79%	165	110	90
S. purpuratus	Animal		907	1,819	176	2,085	40	99%	174	141	133
D. melanogaster	Animal	3.9	120	829	90	1,632	218	25%	279	246	167
A. aegypti	Animal	3.1	1,384	4,614	106	7,752	112	42%	309	252	204
A. gambiae	Animal	3.2	278	1,154	110	2,905	83	26%	286	236	181
A. mellifera	Animal	5.4	454	1,171	107	2,969	98	40%	195	172	153
C. elegans	Animal	5.5	100	259	84	497	176	30%	189	181	151
S. mansoni	Animal	4.8	381	2,222	42	2,387	127	77%	179	167	130
R. oryzae	Fungi	2.3	46	58	66	-	0	1%	201	161	-
C. neoformans	Fungi	5.4	19	64	67	95	8	5%	228	179	56
U. maydis	Fungi	0.8	20	168	134	288	5	18%	256	143	52
S. pombe	Fungi	1.3	13	108	58	-	0	14%	309	102	-
S. cerevisiae	Fungi	0.1	12	241	244	-	0	49%	596	46	-
N. crassa	Fungi	1.8	39	115	126	171	2	11%	206	142	78
M. grisea	Fungi	1.7	42	109	110	103	5	7%	238	160	64
S. nodorum	Fungi	1.7	37	70	82	88	2	3%	257	178	17
A. flavus	Fungi	2.3	40	76	76	76	1	2%	249	161	90
A. nidulans	Fungi	2.8	30	74	87	78	1	2%	204	151	8
H. capsulatum	Fungi	2.5	33	112	114	114	1	8%	227	155	25
C. posadasii	Fungi	2.2	27	80	87	137	10	2%	395	289	81
C. immitis	Fungi	2.5	29	80	83	89	3	2%	349	244	54
S. sclerotiorum	Fungi	1.8	38	84	98	71	7	5%	316	213	56
D. discoideum	Protist	1.3	34	145	107	252	3	13%	265	231	110
P. trichocarpa	Plant	3.1	308	431	140	637	80	50%	204	125	103
A. thaliana	Plant	4.9	119	180	118	242	138	23%	201	143	101
O. sativa	Plant	4.4	371	462	134	725	299	46%	212	135	116
P. patens	Plant	3.8	480	295	188	394	188	57%	220	137	113
C. reinhardtii	Plant	7	118	264	148	376	30	56%	172	121	103
O. lucimarinus	Plant	0.5	13	157	97	-	0	28%	437	135	-
P. infestans	Protist	2	229	76	78	88	5	1%	214	146	92
P. sojae	Protist		86	87	107	75	1	2%	213	147	111
P. yoelii	Protist	1.2	23	179	151	157	1	25%	229	127	18
P. falciparum	Protist	1.8	23	157	119	176	8	24%	189	112	113
P. tetraurelia	Protist	2.5	72	25	26	-	0	0%	246	233	-
T. thermophila	Protist	3.3	104	132	103	136	3	17%	234	166	83
E. histolytica	Protist		23	72	62	-	0	2%	296	168	-
P. tricornutum	Protist	0.8	26	128	109	-	0	12%	446	410	-

*(Number of introns in genome/Number of genes in genome), calculated from genome annotations. ^†The length of the assembly used in our analysis. ^‡Calculated from constitutive introns in EST alignments. ^§Average length of RIs seen in our EST alignments. ^¶See Table S2 in Additional data file 4 for average lengths based on genome annotations. ^¥Average length of the two introns surrounding each predicted CE in our EST alignments. ^#Number of CEs considered for 'Average intron length next to CE' in the previous column and in Figure 5. This excludes those CEs where the introns next to the CEs do not have identical boundaries between transcripts with and without that CE. **Fraction of constitutive introns longer than 200 bp. ^††Calculated from constitutive exons in our EST alignments. ^‡‡Calculated from constitutive exons in our EST alignments (excluding exons that cannot be CEs, namely, the first and last exons in a gene, and exons in genes without introns). ^§§Average length of CEs seen in our EST alignments.

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