Table 5.
BLAST results of a randomly selected set of 26 polymorphic methylated DNA fragments
| MSAP fragment |
Accession No. | Nuclear/protein identity (%) | E value | Sequence homology | |||
| Name | Primer combination | Size (bp) | Chr. | ||||
| M1 | E01/HM37 | 130 | 6 | GenBank:AY785763.1 | 96 | 6.E-42 | Putative polynucleotide adenylyltransferase |
| M2 | E09/HM310 | 233 | 4 | EMBL:CA766808 | 98 | 6.E-66 | IRRI Drought Stress Panicle Library Oryza sativa, cDNA clone |
| GenBank:CI445285.1 | 98 | 2.E-66 | Callus UVB-irradiated callus, 24 h after treatment, cDNA clone | ||||
| M3 | E09/HM311 | 189 | EMBL:AG876068 | O. sativa indica group genomic DNA, BAC end sequence | |||
| M4 | E10/HM311 | 256 | EMBL:AG876068 | 80 | 8.E-46 | O. sativa indica group genomic DNA, BAC end sequence | |
| M5 | E02/HM39 | 157 | 5 | GenBank:AC105768.2 | 95 | 2.E-07 | OJ1122_B08, complete sequence |
| M6 | E10/HM316 | 160 | 1 | GenBank:AP003372.2 | 98 | 4.E-34 | Hypothetical protein |
| M7 | E07/HM313 | 243 | 1 | GenBank:AB254027.1 | 98 | 6.E-53 | atp6 gene for ATPase subunit 6 and ORF79 gene |
| M8 | E08/HM314 | 157 | 4 | GenBank:CK058985.1 | 99 | 1.E-53 | PA64s panicle fertile cDNA |
| M9 | E09/HM312 | 120 | 12 | GenBank:AL731881.4 | 90 | 2.E-23 | Genomic DNA, chromosome 12 (hypothetical protein) |
| M10 | E04/HM37 | 183 | 7 | GenBank:AP005830.4 | 93 | 4.E-74 | Hypothetical protein |
| M11 | E06/HM39 | 90 | 4 | GenBank:AK288604.1 | 90 | 5.E-10 | O. sativa japonica group cDNA |
| EMBL:M22826 | 90 | 2.E-09 | Ribosomal protein L22 (rpL22) gene | ||||
| M12 | E07/HM38 | 272 | 10 | Swiss-Prot:Q10LD3 | 90 | 8.E-23 | Retrotransposon protein, putative, Ty3-gypsy |
| GenBank:AB014740.1 | 93 | 1.E-75 | gypsy-type retrotransposon RIRE8A DNA | ||||
| M13 | E08/HM39 | 297 | 5 | GenBank:BK000929.1 | 96 | 7.E-112 | O. sativa transposon Rim2-M344 |
| Swiss-Prot :Q94I15 | 96 | 6.E-40 | Putative retroelement | ||||
| M14 | E04/HM36 | 200 | 9 | GenBank:CI659730.1 | 94 | 9.E-51 | Leaf of seedling γ-irradiated (4 min), cDNA clone |
| Swiss-Prot :Q9AYB3 | 82 | 2.E-10 | Putative uncharacterized protein | ||||
| M15 | E06/HM33 | 165 | GenBank:AE017283.1 | 98 | 8.E-69 | Aspartyl aminopeptidase | |
| M16 | E10/HM316 | 190 | GenBank:CP000284.1 | 81 | 3.E-18 | N-6 DNA methylase flagellatus | |
| GenBank:AM039952.1 | 73 | 7.E-13 | Type I site-specific deoxyribonuclease | ||||
| M17 | E05/HM312 | 222 | 3 | GenBank:AC136284.1 | 78 | 5.E-35 | Genomic sequence for O. sativa |
| GenBank:CI437782.1 | 72 | 7.E-21 | O. sativa callus UVB-iradiated callus, immediately after treatment | ||||
| GenBank:CI050422.1 | 86 | 1.E-17 | Cold-treated cDNA clone | ||||
| GenBank:CI413574.1 | 86 | 1.E-17 | 100 ppm ZnSO4 for 1 week, cDNA clone | ||||
| GenBank:CI083616.1 | 86 | 1.E-17 | ABA: abscisic acid-treated callus cDNA clone | ||||
| M18 | E05/HM38 | 167 | 10 | GenBank:AC069145 | 100 | 1.E-34 | Genomic sequence |
| M19 | E7/HM310 | 155 | 1 | GenBank:AP003453.3 | 96 | 1.E-53 | O. sativa genomic DNA |
| EMBL:AY873625 | 90 | 4.E-40 | Transposon insertional mutants | ||||
| M20 | E7/HM310 | 143 | 7 | EMBL:EE590765 | 93 | 9.E-63 | Rice, mixture of leaf, root, panicle, cDNA |
| EMBL:EU155081 | 89 | 2.E-38 | Retrotransposon Tos17 | ||||
| M21 | E09/HM32 | 214 | 5 | Swiss-Prot :Q2QMZ1 | 96 | 3.E-25 | HAT family dimerization domain-containing protein, O. sativa |
| M22 | E09/HM32 | 132 | 5 | GenBank:AK289009.1 | 92 | 9.E-35 | O. sativa cDNA, clone: J090089C11 |
| Swiss-Prot :Q2QTE7 | 93 | 5.E-08 | Retrotransposon protein, putative, Ty3-gypsy subclass | ||||
| Swiss-Prot :Q9AYB7 | 93 | 8.E-08 | Similar to Sorghum bicolor 22 kDa akafirincluster | ||||
| M23 | E10/HM32 | 200 | 4 | GenBank:AJ440220.1 | 82 | 1.E-09 | O. sativa a9 gene for plasma membrane H+-ATPase |
| GenBank:CA766881.2 | 77 | 2.E-02 | Drought Stress Panicle Library Indica, cDNA clone | ||||
| M24 | E02/HM31 | 149 | 12 | GenBank:AL713950.4 | 83 | 9.E-23 | BAC OJ1004_F11 |
| GenBank:CB635907.1 | 80 | 6.E-07 | cDNA clone OSIIEb16M12 | ||||
| M25 | E02/HM31 | 90 | GenBank:AK289070.1 | 89 | 4.E-16 | cDNA, clone: J090094F22 | |
| Swiss-Prot :Q5H9W5 | 80 | 3.E-02 | B1168G10.5 protein, O. sativa | ||||
| M26 | E03/HM33 | 209 | 6 | GenBank:AF443596.1 | 93 | 1.E-03 | Zea mays enhancer of zeste-like protein 1 (mez1) mRNA |
| EMBL:EG710286 | 100 | 9.E-06 | Rice young panicle cDNA clone | ||||
Chr., chromosome.