Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here we report AS events deduced from EST/cDNA analysis in two model plants: Arabidopsis and rice. In Arabidopsis, 4,707 (21.8%) of the genes with EST/cDNA evidence show 8,264 AS events. Approximately 56% of these events are intron retention (IntronR), and only 8% are exon skipping. In rice, 6,568 (21.2%) of the expressed genes display 14,542 AS events, of which 53.5% are IntronR and 13.8% are exon skipping. The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. Different AS events within a given gene occur, for the most part, independently. In total, 36-43% of the AS events produce transcripts that would be targets of the non-sense-mediated decay pathway, if that pathway were to operate in plants as in humans. Forty percent of Arabidopsis AS genes are alternatively spliced also in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of posttranscriptional regulation. We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP).
Nucleic Acids Res. 2004 Sep 27;32(17):5096-103
[PMID:
15452276]
Gene. 2005 Jan 3;344:1-20
[PMID:
15656968]
Plant Mol Biol. 2006 Jan;60(1):69-85
[PMID:
16463100]
Mol Cell. 2004 Jan 16;13(1):91-100
[PMID:
14731397]
Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):189-92
[PMID:
12502788]
Genomics. 2003 Dec;82(6):584-95
[PMID:
14611800]
Trends Plant Sci. 2003 Oct;8(10):468-71
[PMID:
14557042]
Nat Genet. 2002 Jan;30(1):29-30
[PMID:
11743582]
Curr Opin Struct Biol. 2004 Jun;14(3):273-82
[PMID:
15193306]
Trends Biochem Sci. 1998 Jun;23(6):198-9
[PMID:
9644970]
Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2850-5
[PMID:
15708978]
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11193-8
[PMID:
11572975]
Bioinformatics. 2004 May 1;20(7):1157-69
[PMID:
14764557]
Plant Mol Biol. 2000 Mar;42(4):571-81
[PMID:
10809003]
Gene. 1994 Apr 20;141(2):171-7
[PMID:
8163185]
Plant Cell. 1989 Aug;1(8):815-25
[PMID:
2535524]
Nucleic Acids Res. 2003 May 15;31(10):2544-52
[PMID:
12736303]
Plant Mol Biol. 1996 Nov;32(3):531-5
[PMID:
8980502]
Annu Rev Biochem. 2003;72:291-336
[PMID:
12626338]
Gene. 2005 Dec 30;364:53-62
[PMID:
16219431]
Trends Plant Sci. 2000 Apr;5(4):160-7
[PMID:
10740297]
Genome Res. 2001 May;11(5):889-900
[PMID:
11337482]
Plant J. 1998 Jul;15(1):125-31
[PMID:
9744100]
Hum Mol Genet. 2003 Jun 1;12(11):1313-20
[PMID:
12761046]
Trends Genet. 2004 Feb;20(2):68-71
[PMID:
14746986]
Genome Biol. 2002;3(6):RESEARCH0029
[PMID:
12093376]
Curr Opin Cell Biol. 2004 Jun;16(3):293-9
[PMID:
15145354]
Plant Cell. 1996 Aug;8(8):1421-35
[PMID:
8776903]
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66
[PMID:
14500829]
Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1908-13
[PMID:
10660679]
Trends Genet. 2005 Feb;21(2):73-7
[PMID:
15661351]
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D354-9
[PMID:
14681433]
Plant Mol Biol. 1998 Mar;36(4):573-83
[PMID:
9484452]
Cell. 1997 May 30;89(5):737-45
[PMID:
9182761]
Plant Physiol. 2005 May;138(1):18-26
[PMID:
15888674]
Plant J. 2005 Aug;43(4):530-40
[PMID:
16098107]
Plant Physiol. 2003 Jun;132(2):469-84
[PMID:
12805580]
Plant J. 1996 Nov;10(5):771-80
[PMID:
8953241]
Curr Opin Cell Biol. 2005 Jun;17(3):309-15
[PMID:
15901502]
Nature. 2002 Nov 21;420(6913):312-6
[PMID:
12447438]
Nat Genet. 2002 Jan;30(1):13-9
[PMID:
11753382]
Nature. 2002 Nov 21;420(6913):316-20
[PMID:
12447439]
Nucleic Acids Res. 1999 Aug 1;27(15):3219-28
[PMID:
10454621]
Nucleic Acids Res. 1995 Jun 25;23(12):2168-77
[PMID:
7610044]
Genome Biol. 2004;5(12):R102
[PMID:
15575968]
J Biol Chem. 1995 Feb 10;270(6):2411-4
[PMID:
7852296]
Plant J. 2004 Sep;39(6):877-85
[PMID:
15341630]
Curr Opin Cell Biol. 2005 Jun;17(3):262-8
[PMID:
15901495]
Plant Mol Biol. 1999 Aug;40(6):1019-30
[PMID:
10527426]
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
[PMID:
9254694]
Bioinformatics. 2004 Nov 1;20(16):2579-85
[PMID:
15117759]
Genome Res. 1999 Dec;9(12):1288-93
[PMID:
10613851]
FEBS Lett. 2000 May 26;474(1):83-6
[PMID:
10828456]
Pac Symp Biocomput. 2004;:66-77
[PMID:
14992493]
Bioinformatics. 2005 Nov 1;21 Suppl 3:iii20-30
[PMID:
16306388]
Nucleic Acids Res. 2001 Jul 1;29(13):2850-9
[PMID:
11433032]
PLoS Biol. 2005 Feb;3(2):e38
[PMID:
15685292]
