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Table 2 Genes with AS events covered by at least 30 ESTs and where each choice is about equally supported.

From: Prevalence of alternative splicing choices in Arabidopsis thaliana

Locus Abbreviated Description (TAIR) GA ESTs GA GP ESTs GP AS type Size DR %
MF
AT5G36290 Uncharacterised protein family UPF0016 (InterPro: IPR001727) .1 30 .2 16 RI 100
(U)
34
AT5G62000 Encodes an auxin response factor. Mutants have ... defects including enlarged rosette leaves, reduced fertility, later senescence, hypocotyl elongation defects, enlarged seeds and enlarged cotyledons... Increase in seed size due to increased cell proliferation. .2 16 .3 20 AS 3
(U)
44
AT5G58330 malate dehydrogenase (NADP), chloroplast, putative; FUNCTIONS IN: oxidoreductase activity .2 33 .1 62 AS 3
(P)
35
AT5G66240 transducin family protein/WD-40 repeat family protein; FUNCTIONS IN: nucleotide binding; LOCATED IN: CUL4 RING ubiquitin ligase complex .1 13 .2 25 RI 89
(P)
34
AT5G64200 encodes an SC35-like splicing factor ... localized to the nuclear specks. .1 10 .2 22 RI 190
(U)
31
AT4G35450 Involved in targeting of chloroplast outer membrane proteins to the chloroplast. Double mutants of AKR2A and the highly homologous AKR2B have yellow leaves, significantly reduced chloroplast proteins, and no thylakoid membranes. .1 32 .3 39 DS 44
(U)
45
AT4G36690 ATU2AF65A; FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: nuclear mRNA splicing...defence response to bacterium .1 21 .2 17 RI 273
(P)
45
AT4G30760 Unknown .2 19 .1 26 AS 3
(P)
42
AT4G16162 CONTAINS InterPro DOMAIN/s: Leucine-rich repeat (InterPro:IPR001611); BEST A. thaliana ... match is: serine/threonine protein kinase-related .2 15 .3 15 ES 58
(P)
50
AT3G23830 encodes a glycine-rich RNA binding protein. Gene expression is induced by cold and reduced by ionic (salt) and non-ionic (mannitol) osmotic stress. Lines overexpressing the gene are slightly more tolerant to osmotic stress during germination. .2 21 .1 17 AS 12
(U)
45
AT3G01540 RNA HELICASE DRH1 .1 28 .2 32 AS 3
(P)
47
AT3G62840 LOCATED IN: small nucleolar ribonucleoprotein complex, nucleus; CONTAINS InterPro DOMAIN/s: Like-Sm ribonucleoproteinBEST A. thaliana protein match is: small nuclear ribonucleoprotein D2, putative/snRNP core protein D2, .2 16 .1 18 AS 3
(P)
47
AT2G05990 Encodes enoyl-ACP reductase a component of the fatty acid synthase complex. A reduced function mutation in this gene, mod1, was found in a screen for premature cell death mutants. Mutant plants have reduced lipid level and pleiotropic morphological defects, including chlorotic and abnormally shaped leaves .2 24 .1 33 AS 3
(U)
42
AT2G19730 60 S ribosomal protein L28 (RPL28A) .2 63 .1 67 AS 4
(U)
49
AT2G17442 Unknown .4 13 .1 24 AS 3
(P)
35
AT2G17442 Unknown .4 23 .3 12 DS 31
(U)
34
AT2G39730 Rubisco activase, a nuclear-encoded chloroplast protein that consists of two isoforms arising from alternative splicing in most plants. .1 201 .2 187 AS 11
(P)
48
AT1G64750 Unknown .1 18 .2 20 RI 90
(U)
47
AT1G67700 Unknown .2 22 .1 18 DS 14
(P)
45
AT1G69510 Unknown .1 22 .3 13 AS 5
(U)
37
AT1G71470 Unknown .2 21 .1 9 AS 9
(P)
30
AT1G80380 encodes a glycerate kinase which catalyzes the last step of photorespiration C2 cycle .2 26 .3 13 DS 57
(P)
33
AT1G26850 dehydration-responsive family protein; LOCATED IN: Golgi apparatus, membrane; CONTAINS InterPro DOMAIN/s: methyltransferase putative .2 9 .3 21 DS 64
(U)
30
  1. Functional descriptions are from the version of the TAIR Web site. Columns labelled GA and GP indicate which gene models (using TAIR suffixes) correspond to the Gene Absent and Gene Present variations, respectively. ESTs GA and ESTs GP contain the number of spliced ESTs supporting the GA or GP splicing pattern. AS type refers the type of alternative splicing involved in the AS event. RI means retained intron; AS means alternative acceptor site (3-prime boundary of an intron); DS means alternative donor site (5-prime boundary of an intron); ES means exon skipping. The column titled Size DR gives the size of the Difference Region and whether it changes protein-coding sequence (P) or untranslated (U) region of the gene models. The last column (titled % MF) gives the percentage of overlapping ESTs (ESTs GA and ESTs GP) that support the less commonly observed (minor) form.