Table 2.
Genes/transcripts with significant changes in the ratio of alternatively spliced isoforms in AtGRP7-ox plants
| primer pair | AGI | Description | Product sizes (bp) | Col-2 |
AtGRP7-ox (Col-2) |
P-value | C24 |
AtGRP7-ox (C24) |
P-value | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Small prod. (%) | Large prod. (%) | Small prod. (%) | Large prod. (%) | 7-ox (Col-2) | Small prod. (%) | Large prod. (%) | Small prod. (%) | Large prod. (%) | 7-ox (C24) | ||||
| Alternative 3′SS | |||||||||||||
| 12 | At1g72320 | APUM23 (Arabidopsis pumilio 23); RNA binding | 141/150/215 | 15 | 83 | 5 | 95 | 0.0002 | 23 | 74 | 8 | 92 | 0.0192 |
| 19 | At2g32320 | tRNA His guanylyltransferase | 202/273 | 33 | 67 | 45 | 55 | 0.0047 | 31 | 69 | 39 | 61 | 0.0048 |
| 36 | At4g12790 | ATP-binding family protein | 212/338 | 45 | 55 | 25 | 75 | 0.0029 | 46 | 54 | 25 | 75 | 0.0034 |
| 49 | At5g41150 | UVH1 (ultraviolet hypersensitive 1) | 293/346 | 82 | 18 | 72 | 28 | 0.0003 | 92 | 8 | 84 | 16 | 0.0034 |
| 59 | At5g66010 | RNA binding | 105/182 | 30 | 70 | 40 | 60 | 0.0261 | 38 | 62 | 59 | 41 | 0.0016 |
| 242 | At1g60850 | ATRPAC42 (Arabidopsis thaliana RNA polymerase I subunit 42); DNA binding/DNA-directed RNA polymerase | 111/122 | 70 | 30 | 77 | 23 | 0.0311 | 73 | 27 | 79 | 21 | 0.0325 |
| 254 | At5g50240 | l-isospartyl methyltransferase | 192/201 | 63 | 37 | 73 | 27 | 0.0282 | 64 | 36 | 73 | 27 | 0.0079 |
| 273 | At3g07810 | Heterogeneous nuclear ribonucleoprotein, putative/hnRNP, putative | 126/173 | 8 | 92 | 3 | 97 | 0.0094 | 10 | 90 | 4 | 96 | 0.0372 |
| 288 | At3g12570 | FYD | 159/188 | 43 | 57 | 52 | 48 | 0.0148 | 39 | 61 | 53 | 47 | 0.0207 |
| 295 | At2g02390 | ATGSTZ1 (glutathione s-transferase 18); glutathione transferase | 181/202 | 88 | 12 | 69 | 31 | 0.0023 | 87 | 13 | 71 | 29 | 0.0016 |
| 378 | At3g62190 | DNAJ heat shock N-terminal domain-containing protein | 144/334 | 89 | 11 | 99 | 1 | 0.0075 | 85 | 15 | 98 | 2 | 0.0032 |
| Alternative 5′SS | |||||||||||||
| 72 | At2g04790 | Similar to unnamed protein product [Vitis vinifera] (GB:CAO23994.1) | 167/190 | 68 | 32 | 53 | 47 | 0.0077 | 41 | 59 | 29 | 71 | 0.0027 |
| 75 | At2g36000 | Mitochondrial transcription termination factor-related/mTERF-related | 150/254 | 31 | 69 | 14 | 86 | 0.0009 | 40 | 60 | 17 | 83 | 0.0016 |
| 87 | At4g35450 | AKR2 (ankyrin repeat-containing protein 2); protein binding | 305/350 | 78 | 22 | 59 | 41 | 0.0052 | 72 | 28 | 57 | 43 | 0.0009 |
| 90 | At4g39260 | ATGRP8/GR-RBP8 (CCR1) | 158/316 | 94 | 6 | 23 | 77 | 0.0000 | 97 | 3 | 23 | 77 | 0.0004 |
| 112 | At1g09530 | PAP3/PIF3/POC1 (phytochrome interacting factor 3); DNA binding/protein binding/transcription factor | 230/290 | 88 | 12 | 59 | 41 | 0.0000 | 90 | 10 | 66 | 34 | 0.0033 |
| 129 | At2g40830 | RHC1A (RING-H2 finger C1A); protein binding/zinc ion binding | 220/329 | 91 | 9 | 59 | 41 | 0.0012 | 91 | 9 | 63 | 37 | 0.0037 |
| 136 | At3g07740 | ADA2A (Arabidopsis adaptor 2A homolog); DNA binding/transcription factor | 139/240 | 100 | 0 | 46 | 54 | 0.0006 | 100 | 0 | 70 | 30 | 0.0063 |
| 141 | At3g51880 | HMGB1 (High mobility group B 1); transcription factor | 204/225 | 92 | 8 | 79 | 21 | 0.0471 | 92 | 8 | 87 | 13 | 0.0003 |
| 145 | At3g17609 | HYH (Hy5-homolog); DNA binding/transcription factor | 150/153/195/268 | 32 | 68 | 54 | 46 | 0.0197 | 29 | 71 | 44 | 56 | 0.0275 |
| 148 | At1g76510 | ARID/BRIGHT DNA-binding domain-containing protein | 189/212 | 28 | 72 | 16 | 84 | 0.0073 | 37 | 63 | 25 | 75 | 0.0006 |
| 149 | At2g27230 | Transcription factor-related | 208/246 | 28 | 72 | 18 | 82 | 0.0177 | 34 | 66 | 22 | 78 | 0.0060 |
| 189 | At5g43270 | SPL2 (squamosa promoter binding protein-like 2); DNA binding/transcription factor | 160/244 | 87 | 13 | 63 | 37 | 0.0021 | 87 | 13 | 69 | 31 | 0.0044 |
| 261 | At4g10100 | CNX7/SIR5; catalytic | 254/270 | 58 | 42 | 46 | 54 | 0.0007 | 58 | 42 | 45 | 55 | 0.0028 |
| 272 | At3g23900 | RNA recognition motif (RRM)-containing protein | 118/125 | 30 | 70 | 22 | 78 | 0.0008 | 30 | 70 | 23 | 77 | 0.0041 |
| 285 | At3g19840 | FF domain-containing protein/WW domain-containing protein | 171/207 | 61 | 39 | 40 | 60 | 0.0004 | 65 | 35 | 43 | 57 | 0.0084 |
| 322 | At2g33480 | ANAC041 (Arabidopsis NAC domain containing protein 41); transcription factor | 321/399 | 17 | 83 | 34 | 66 | 0.0047 | 15 | 85 | 29 | 71 | 0.0025 |
| 324 | At5g43270 | SPL2 (squamosa promoter binding protein-like 2); DNA binding/transcription factor | 186/270 | 86 | 14 | 66 | 34 | 0.0046 | 95 | 5 | 66 | 34 | 0.0158 |
| 343 | At3g29160 | AKIN11 (Arabidopsis snf1 kinase homolog 11); protein kinase | 159/307 | 30 | 70 | 3 | 97 | 0.0008 | 45 | 55 | 2 | 98 | 0.0009 |
| Exon skipping | |||||||||||||
| 181 | At5g05550 | Transcription factor | 210/308 | 64 | 36 | 74 | 26 | 0.0143 | 59 | 41 | 75 | 25 | 0.0044 |
| 196 | At3g01150 | PTB (polypyrimidine tract-binding); RNA binding | 165/268 | 91 | 9 | 97 | 3 | 0.0035 | 92 | 8 | 97 | 3 | 0.0071 |
| 226 | At4g24740 | AFC2 (Arabidopsis fus3-complementing gene 1); kinase | 143/309 | 19 | 81 | 47 | 53 | 0.0020 | 12 | 88 | 45 | 55 | 0.0004 |
| 227 | At4g24740 | AFC2 (Arabidopsis fus3-complementing gene 1); kinase | 152/343 | 30 | 70 | 73 | 27 | 0.0000 | 33 | 67 | 68 | 32 | 0.0005 |
| 380 | At5g08185 | npcRNA 78; MIR162a | 103/168 | 64 | 36 | 42 | 58 | 0.0044 | 83 | 17 | 75 | 25 | 0.0267 |
| Intron retention | |||||||||||||
| 327 | At5g59950 | RNA and export factor-binding protein, putative | 226/422 | 84 | 16 | 50 | 50 | 0.0020 | 93 | 7 | 69 | 31 | 0.0091 |
The two AS isoforms considered here are underlined.