6 variations found. Os11g0116600/LOC_Os11g02470 (WRKY52; expressed), ranging from 749,997 bp to 751,210 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g02470 | OsWRKY52 - Superfamily of TFs having WRKY and zinc finger domains, expressed; RAP ID: Os11g0116600; MSU ID: LOC_Os11g02470 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os11g02470 | Os11g0116600 | OsWRKY52 | Rice WRKY gene52 | BK005055. WRKY7 in Zhang and Wang (2005) and in Berri et al. (2009). WRKY87 in Wu et al. (2005). | WRKY52 | WRKY GENE 52 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg1100750466 (J) | chr11 | 750466 | G | C | 59.80% | 0.04% | C -> G |
mr1016 (Ind_All); LR P-value: 8.93E-14;
mr1017 (Ind_All); LR P-value: 2.58E-12; mr1022 (Ind_All); LR P-value: 2.80E-12; mr1023 (Ind_All); LR P-value: 5.34E-10; mr1055 (Ind_All); LR P-value: 4.50E-15; mr1079 (Ind_All); LR P-value: 1.08E-13; mr1082 (Ind_All); LR P-value: 4.10E-07; mr1093 (Ind_All); LR P-value: 4.94E-08; mr1103 (Ind_All); LR P-value: 1.93E-06; mr1132 (Ind_All); LR P-value: 4.06E-13; mr1142 (Ind_All); LR P-value: 4.11E-11; mr1178 (Ind_All); LR P-value: 2.98E-12; mr1226 (Ind_All); LR P-value: 1.46E-07; mr1249 (All); LR P-value: 8.23E-08; mr1301 (Ind_All); LR P-value: 2.28E-10; mr1390 (Ind_All); LR P-value: 5.59E-13; mr1410 (Ind_All); LR P-value: 2.87E-08; mr1489 (Ind_All); LR P-value: 4.69E-07; mr1490 (Ind_All); LR P-value: 2.57E-12; mr1491 (Ind_All); LR P-value: 6.99E-11; mr1546 (Ind_All); LR P-value: 2.06E-09; mr1558 (All); LR P-value: 2.63E-49; mr1609 (All); LR P-value: 9.40E-12; mr1805 (Ind_All); LR P-value: 1.97E-07; mr1022_2 (Ind_All); LR P-value: 1.25E-13; mr1023_2 (Ind_All); LR P-value: 1.63E-11; mr1055_2 (Ind_All); LR P-value: 2.43E-14; mr1079_2 (Ind_All); LR P-value: 6.74E-14; mr1093_2 (Ind_All); LR P-value: 6.64E-08; mr1132_2 (Ind_All); LR P-value: 7.40E-14; mr1178_2 (Ind_All); LR P-value: 1.34E-14; mr1390_2 (Ind_All); LR P-value: 1.75E-14; mr1489_2 (Ind_All); LR P-value: 4.00E-08; mr1490_2 (Ind_All); LR P-value: 6.25E-14; mr1509_2 (All); LR P-value: 1.57E-46; mr1558_2 (All); LR P-value: 1.65E-58; mr1609_2 (All); LR P-value: 6.85E-22 |
LOC_Os11g02470.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g02470.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 65.858; most accessible tissue: Minghui63 panicle, score: 89.702 |
| vg1100750797 (J) | chr11 | 750797 | T | C | 56.20% | 0.02% | C -> T |
mr1016 (Ind_All); LR P-value: 1.30E-13;
mr1017 (Ind_All); LR P-value: 6.01E-12; mr1022 (Ind_All); LR P-value: 7.13E-13; mr1023 (Ind_All); LR P-value: 3.85E-10; mr1026 (All); LR P-value: 3.39E-36; mr1055 (Ind_All); LR P-value: 6.82E-14; mr1063 (All); LR P-value: 6.70E-50; mr1079 (Ind_All); LR P-value: 2.51E-13; mr1082 (Ind_All); LR P-value: 2.55E-07; mr1083 (All); LR P-value: 9.42E-23; mr1085 (All); LR P-value: 1.21E-29; mr1093 (Ind_All); LR P-value: 5.00E-09; mr1103 (Ind_All); LR P-value: 3.47E-06; mr1109 (All); LR P-value: 1.58E-52; mr1129 (All); LR P-value: 8.94E-36; mr1132 (Ind_All); LR P-value: 3.35E-12; mr1139 (All); LR P-value: 1.35E-38; mr1142 (Ind_All); LR P-value: 2.68E-11; mr1161 (All); LR P-value: 5.09E-37; mr1169 (All); LR P-value: 4.65E-12; mr1178 (Ind_All); LR P-value: 3.58E-13; mr1226 (All); LR P-value: 1.82E-29; mr1241 (Ind_All); LR P-value: 3.01E-06; mr1255 (All); LR P-value: 1.09E-17; mr1257 (All); LR P-value: 5.45E-32; mr1260 (All); LR P-value: 2.87E-08; mr1261 (All); LR P-value: 8.62E-16; mr1264 (All); LR P-value: 2.12E-24; mr1301 (Ind_All); LR P-value: 1.45E-10; mr1316 (All); LR P-value: 1.28E-10; mr1390 (Ind_All); LR P-value: 5.43E-13; mr1410 (Ind_All); LR P-value: 1.56E-08; mr1411 (All); LR P-value: 4.28E-26; mr1411 (Ind_All); LR P-value: 3.58E-07; mr1416 (All); LR P-value: 2.22E-21; mr1435 (All); LR P-value: 3.88E-36; mr1437 (All); LR P-value: 1.48E-40; mr1489 (Ind_All); LR P-value: 5.61E-07; mr1490 (Ind_All); LR P-value: 3.81E-12; mr1491 (Ind_All); LR P-value: 1.25E-11; mr1546 (Ind_All); LR P-value: 6.25E-09; mr1551 (All); LR P-value: 2.15E-25; mr1558 (All); LR P-value: 6.84E-48; mr1560 (All); LR P-value: 2.88E-30; mr1657 (All); LR P-value: 4.50E-11; mr1805 (Ind_All); LR P-value: 8.77E-08; mr1807 (All); LR P-value: 4.08E-16; mr1870 (All); LR P-value: 9.06E-16; mr1883 (All); LR P-value: 4.80E-11; mr1970 (All); LR P-value: 8.28E-62; mr1973 (All); LR P-value: 2.98E-79; mr1022_2 (Ind_All); LR P-value: 4.99E-13; mr1023_2 (Ind_All); LR P-value: 7.84E-11; mr1055_2 (Ind_All); LR P-value: 1.96E-13; mr1079_2 (Ind_All); LR P-value: 2.11E-13; mr1083_2 (All); LR P-value: 5.66E-32; mr1088_2 (All); LR P-value: 1.39E-73; mr1089_2 (All); LR P-value: 1.59E-50; mr1089_2 (Ind_All); LR P-value: 3.51E-07; mr1093_2 (Ind_All); LR P-value: 4.23E-09; mr1109_2 (All); LR P-value: 1.36E-61; mr1129_2 (All); LR P-value: 8.57E-38; mr1132_2 (Ind_All); LR P-value: 9.40E-14; mr1161_2 (All); LR P-value: 8.25E-36; mr1178_2 (Ind_All); LR P-value: 4.34E-15; mr1226_2 (All); LR P-value: 1.46E-39; mr1235_2 (Ind_All); LR P-value: 3.61E-08; mr1243_2 (Ind_All); LR P-value: 8.36E-06; mr1251_2 (All); LR P-value: 2.30E-37; mr1253_2 (All); LR P-value: 1.06E-20; mr1255_2 (All); LR P-value: 9.37E-22; mr1257_2 (All); LR P-value: 3.68E-35; mr1270_2 (All); LR P-value: 2.91E-27; mr1316_2 (All); LR P-value: 1.13E-22; mr1390_2 (Ind_All); LR P-value: 5.79E-14; mr1435_2 (All); LR P-value: 1.30E-37; mr1489_2 (Ind_All); LR P-value: 4.86E-08; mr1490_2 (Ind_All); LR P-value: 1.98E-13; mr1509_2 (All); LR P-value: 4.59E-47; mr1531_2 (All); LR P-value: 5.56E-20; mr1551_2 (All); LR P-value: 1.11E-21; mr1558_2 (All); LR P-value: 5.15E-57; mr1599_2 (Ind_All); LR P-value: 9.54E-09; mr1720_2 (All); LR P-value: 2.11E-17; mr1807_2 (All); LR P-value: 1.14E-14; mr1870_2 (All); LR P-value: 6.62E-17; mr1913_2 (All); LR P-value: 4.06E-31; mr1932_2 (All); LR P-value: 4.00E-30 |
LOC_Os11g02464.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02470.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 68.942; most accessible tissue: Callus, score: 86.605 |
| vg1100750948 (J) | chr11 | 750948 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os11g02470.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os11g02464.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.884; most accessible tissue: Zhenshan97 root, score: 87.187 |
| vg1100750967 (J) | chr11 | 750967 | T | A | 59.80% | 0.08% | A -> T |
LOC_Os11g02470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g02470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.805; most accessible tissue: Zhenshan97 root, score: 87.558 |
|
| vg1100750972 (J) | chr11 | 750972 | A | G | 96.60% | 0.00% | A -> G | NA |
LOC_Os11g02470.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.957; most accessible tissue: Zhenshan97 root, score: 87.647 |
| vg1100750983 (J) | chr11 | 750983 | A | G | 59.80% | 0.11% | G -> A |
LOC_Os11g02470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g02470.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.762; most accessible tissue: Zhenshan97 root, score: 87.647 |