42 variations found. Os04g0567800/LOC_Os04g47990 (dof zinc finger domain containing protein; putative; expressed), ranging from 28,534,299 bp to 28,537,554 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g47990 | dof zinc finger domain containing protein, putative, expressed; RAP ID: Os04g0567800; MSU ID: LOC_Os04g47990 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0428536667 (J) | chr04 | 28536667 | AAGGAAG GAAGGAA | AAGGAAG GAA | 59.60% | 0.00% | AAGGAAGGAA -> AAGGAAGGAA GGAA | NA |
|
| STR0428536782 (J) | chr04 | 28536782 | CTACT | CTACT | 99.00% | 0.00% | CTACT -> CTACC | NA |
|
| STR0428536911 (J) | chr04 | 28536911 | GTGTGTG TGTGTGT G | GTGTGTG TGTGTGT GTG | 94.60% | 0.00% | GTGTGTGTGT GTGTG -> GTGTGTGTGT GTGTGTG | NA |
|
| STR0428537336 (J) | chr04 | 28537336 | CC | CCC | 60.50% | 0.00% | CCC -> CC | NA |
|
| vg0428534413 (J) | chr04 | 28534413 | AC | A | 98.60% | 0.00% | AC -> A | NA |
LOC_Os04g47990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.038; most accessible tissue: Zhenshan97 panicle, score: 97.147 |
| vg0428534560 (J) | chr04 | 28534560 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os04g47990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.805; most accessible tissue: Zhenshan97 panicle, score: 97.661 |
| vg0428534728 (J) | chr04 | 28534728 | G | A | 97.50% | 0.00% | G -> A | NA |
LOC_Os04g47990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.161; most accessible tissue: Zhenshan97 panicle, score: 97.742 |
| vg0428534736 (J) | chr04 | 28534736 | C | A | 95.70% | 0.00% | C -> A | NA |
LOC_Os04g47990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.553; most accessible tissue: Zhenshan97 panicle, score: 97.761 |
| vg0428534750 (J) | chr04 | 28534750 | C | G | 60.00% | 0.02% | G -> C |
LOC_Os04g47990.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.481; most accessible tissue: Zhenshan97 panicle, score: 97.761 |
|
| vg0428534860 (J) | chr04 | 28534860 | T | C | 51.80% | 0.02% | C -> T |
mr1013 (All); LR P-value: 4.92E-13;
mr1037 (All); LR P-value: 3.59E-30; mr1053 (All); LR P-value: 6.59E-07; mr1064 (All); LR P-value: 3.28E-37; mr1065 (All); LR P-value: 9.18E-58; mr1067 (All); LR P-value: 2.81E-44; mr1068 (All); LR P-value: 1.20E-56; mr1076 (All); LR P-value: 1.61E-27; mr1078 (All); LR P-value: 4.78E-52; mr1083 (All); LR P-value: 4.51E-24; mr1087 (All); LR P-value: 2.56E-55; mr1090 (All); LR P-value: 6.09E-55; mr1091 (All); LR P-value: 2.70E-38; mr1094 (All); LR P-value: 9.98E-37; mr1096 (All); LR P-value: 6.18E-53; mr1104 (All); LR P-value: 3.45E-33; mr1108 (All); LR P-value: 2.84E-50; mr1109 (All); LR P-value: 1.93E-46; mr1110 (All); LR P-value: 2.72E-36; mr1111 (All); LR P-value: 1.37E-52; mr1112 (All); LR P-value: 1.41E-48; mr1121 (All); LR P-value: 1.05E-49; mr1125 (All); LR P-value: 4.99E-49; mr1131 (All); LR P-value: 3.32E-21; mr1139 (All); LR P-value: 8.94E-40; mr1144 (All); LR P-value: 1.36E-46; mr1145 (All); LR P-value: 1.00E-27; mr1147 (All); LR P-value: 1.79E-17; mr1169 (All); LR P-value: 7.51E-14; mr1179 (All); LR P-value: 9.85E-19; mr1181 (All); LR P-value: 2.03E-27; mr1195 (All); LR P-value: 4.86E-10; mr1199 (All); LR P-value: 5.68E-16; mr1200 (All); LR P-value: 7.64E-44; mr1204 (All); LR P-value: 1.55E-31; mr1208 (All); LR P-value: 3.61E-30; mr1211 (All); LR P-value: 9.99E-50; mr1224 (All); LR P-value: 1.01E-30; mr1225 (All); LR P-value: 5.78E-32; mr1226 (All); LR P-value: 3.64E-29; mr1234 (All); LR P-value: 4.09E-48; mr1237 (All); LR P-value: 1.12E-31; mr1244 (All); LR P-value: 4.07E-21; mr1257 (All); LR P-value: 5.64E-30; mr1264 (All); LR P-value: 3.52E-25; mr1270 (All); LR P-value: 1.35E-13; mr1299 (All); LR P-value: 1.29E-09; mr1321 (All); LR P-value: 1.09E-06; mr1342 (All); LR P-value: 6.03E-10; mr1404 (All); LR P-value: 3.12E-34; mr1411 (All); LR P-value: 2.77E-25; mr1416 (All); LR P-value: 2.80E-23; mr1426 (All); LR P-value: 3.73E-32; mr1436 (All); LR P-value: 3.20E-30; mr1437 (All); LR P-value: 1.40E-40; mr1458 (All); LR P-value: 3.53E-44; mr1526 (All); LR P-value: 1.14E-46; mr1534 (All); LR P-value: 1.01E-40; mr1537 (All); LR P-value: 2.43E-24; mr1551 (All); LR P-value: 3.06E-27; mr1552 (All); LR P-value: 1.94E-19; mr1560 (All); LR P-value: 1.13E-31; mr1620 (All); LR P-value: 2.06E-40; mr1655 (All); LR P-value: 8.74E-15; mr1657 (All); LR P-value: 3.63E-11; mr1671 (All); LR P-value: 5.02E-62; mr1689 (All); LR P-value: 8.17E-21; mr1700 (All); LR P-value: 3.41E-16; mr1713 (All); LR P-value: 1.68E-11; mr1717 (All); LR P-value: 3.78E-07; mr1721 (All); LR P-value: 2.50E-39; mr1733 (Ind_All); LR P-value: 6.75E-06; mr1745 (All); LR P-value: 5.42E-33; mr1748 (All); LR P-value: 1.84E-06; mr1756 (All); LR P-value: 4.33E-07; mr1770 (All); LR P-value: 1.02E-09; mr1793 (All); LR P-value: 2.36E-29; mr1798 (All); LR P-value: 2.01E-55; mr1819 (All); LR P-value: 7.42E-11; mr1841 (All); LR P-value: 3.92E-23; mr1877 (All); LR P-value: 2.50E-26; mr1878 (All); LR P-value: 1.93E-35; mr1883 (All); LR P-value: 8.56E-13; mr1916 (All); LR P-value: 4.98E-16; mr1938 (All); LR P-value: 4.14E-12; mr1970 (All); LR P-value: 2.05E-69; mr1973 (All); LR P-value: 6.48E-87; mr1037_2 (All); LR P-value: 3.73E-31; mr1065_2 (All); LR P-value: 6.44E-68; mr1067_2 (All); LR P-value: 1.50E-57; mr1068_2 (All); LR P-value: 4.96E-67; mr1078_2 (All); LR P-value: 1.06E-64; mr1090_2 (All); LR P-value: 1.10E-59; mr1091_2 (All); LR P-value: 4.24E-50; mr1094_2 (All); LR P-value: 1.46E-45; mr1096_2 (All); LR P-value: 1.28E-60; mr1108_2 (All); LR P-value: 2.84E-57; mr1110_2 (All); LR P-value: 5.84E-39; mr1111_2 (All); LR P-value: 9.28E-55; mr1112_2 (All); LR P-value: 1.61E-65; mr1121_2 (All); LR P-value: 1.08E-52; mr1144_2 (All); LR P-value: 8.08E-57; mr1164_2 (All); LR P-value: 5.43E-21; mr1200_2 (All); LR P-value: 1.10E-52; mr1208_2 (All); LR P-value: 1.62E-36; mr1234_2 (All); LR P-value: 1.29E-60; mr1244_2 (All); LR P-value: 4.61E-27; mr1458_2 (All); LR P-value: 4.63E-49; mr1509_2 (All); LR P-value: 1.66E-45; mr1551_2 (All); LR P-value: 7.28E-22; mr1571_2 (All); LR P-value: 8.61E-33; mr1744_2 (All); LR P-value: 2.22E-15; mr1745_2 (All); LR P-value: 5.02E-41; mr1793_2 (All); LR P-value: 3.47E-51; mr1798_2 (All); LR P-value: 3.93E-78; mr1877_2 (All); LR P-value: 1.16E-21; mr1970_2 (All); LR P-value: 3.47E-65; mr1973_2 (All); LR P-value: 8.26E-101 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g47990.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g47990.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.807; most accessible tissue: Zhenshan97 panicle, score: 97.252 |
| vg0428535026 (J) | chr04 | 28535026 | A | G | 54.50% | 0.04% | G -> A |
mr1076 (All); LR P-value: 1.51E-26;
mr1083 (All); LR P-value: 9.53E-23; mr1108 (All); LR P-value: 2.56E-44; mr1169 (All); LR P-value: 2.68E-13; mr1179 (All); LR P-value: 3.24E-18; mr1181 (All); LR P-value: 4.00E-26; mr1195 (All); LR P-value: 1.84E-10; mr1264 (All); LR P-value: 1.16E-23; mr1281 (All); LR P-value: 1.06E-10; mr1342 (All); LR P-value: 1.91E-09; mr1362 (All); LR P-value: 4.76E-13; mr1416 (All); LR P-value: 3.21E-22; mr1426 (All); LR P-value: 3.99E-30; mr1436 (All); LR P-value: 7.07E-29; mr1526 (All); LR P-value: 2.27E-42; mr1551 (All); LR P-value: 3.66E-24; mr1560 (All); LR P-value: 1.47E-30; mr1581 (All); LR P-value: 3.30E-10; mr1620 (All); LR P-value: 1.76E-39; mr1655 (All); LR P-value: 8.23E-14; mr1671 (All); LR P-value: 8.17E-59; mr1689 (All); LR P-value: 4.98E-21; mr1733 (Ind_All); LR P-value: 6.75E-06; mr1770 (All); LR P-value: 9.39E-09; mr1798 (All); LR P-value: 3.23E-50; mr1819 (All); LR P-value: 6.01E-11; mr1841 (All); LR P-value: 5.78E-23; mr1878 (All); LR P-value: 2.69E-33; mr1883 (All); LR P-value: 1.08E-13; mr1916 (All); LR P-value: 3.89E-15; mr1065_2 (All); LR P-value: 1.43E-63; mr1111_2 (All); LR P-value: 7.56E-49; mr1509_2 (All); LR P-value: 1.99E-45; mr1798_2 (All); LR P-value: 8.22E-71 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g47990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g47990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.806; most accessible tissue: Zhenshan97 panicle, score: 94.740 |
| vg0428535065 (J) | chr04 | 28535065 | AAAG | AAAGAAG | 95.60% | 0.00% | AAAG -> AAAGAAG,A | NA |
LOC_Os04g47990.1 Alt: AAAGAAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.2 Alt: AAAGAAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g47990.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g47990.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.003; most accessible tissue: Zhenshan97 panicle, score: 94.880 |
| vg0428535330 (J) | chr04 | 28535330 | T | G | 58.80% | 0.00% | G -> T |
LOC_Os04g47990.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g47990.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.173; most accessible tissue: Zhenshan97 panicle, score: 95.548 |
|
| vg0428535375 (J) | chr04 | 28535375 | G | A | 95.70% | 0.00% | G -> A | NA |
LOC_Os04g47990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g47990.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.516; most accessible tissue: Zhenshan97 panicle, score: 95.756 |
| vg0428535393 (J) | chr04 | 28535393 | G | T | 98.90% | 0.00% | G -> T | NA |
LOC_Os04g47990.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g47990.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 84.246; most accessible tissue: Zhenshan97 panicle, score: 95.903 |
| vg0428535449 (J) | chr04 | 28535449 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os04g47990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g47990.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 85.307; most accessible tissue: Zhenshan97 panicle, score: 95.654 |
| vg0428535672 (J) | chr04 | 28535672 | T | C | 58.70% | 0.00% | C -> T |
LOC_Os04g47990.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g47990.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.455; most accessible tissue: Zhenshan97 panicle, score: 96.452 |
|
| vg0428535746 (J) | chr04 | 28535746 | TTGG | CTGG | 98.90% | 0.00% | TTGG -> CTGG,T | NA |
LOC_Os04g47990.1 Alt: CTGG| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g47990.2 Alt: CTGG| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os04g47990.1 Alt: T| inframe_deletion MODERATE(snpEff) LOC_Os04g47990.2 Alt: T| inframe_deletion MODERATE(snpEff) The average chromatin accessibility score: 85.078; most accessible tissue: Zhenshan97 panicle, score: 95.756 |
| vg0428536062 (J) | chr04 | 28536062 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os04g47990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g47990.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 84.845; most accessible tissue: Zhenshan97 panicle, score: 95.323 |
| vg0428536201 (J) | chr04 | 28536201 | C | T | 94.10% | 0.00% | C -> T | NA |
LOC_Os04g47990.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os04g47990.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 88.570; most accessible tissue: Zhenshan97 panicle, score: 95.903 |
| vg0428536248 (J) | chr04 | 28536248 | A | G | 59.00% | 0.00% | G -> A | NA |
LOC_Os04g47990.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g47990.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.469; most accessible tissue: Zhenshan97 panicle, score: 95.654 |
| vg0428536391 (J) | chr04 | 28536391 | C | A | 98.80% | 0.00% | C -> A | NA |
LOC_Os04g47990.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.882; most accessible tissue: Zhenshan97 panicle, score: 96.769 |
| vg0428536651 (J) | chr04 | 28536651 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os04g47990.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.266; most accessible tissue: Minghui63 panicle, score: 98.225 |
| vg0428536664 (J) | chr04 | 28536664 | CGAAA | C | 59.90% | 0.00% | C -> CGAAA | NA |
LOC_Os04g47990.2 Alt: CGAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g47990.1 Alt: CGAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.281; most accessible tissue: Minghui63 panicle, score: 98.240 |
| vg0428536670 (J) | chr04 | 28536670 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os04g47990.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g47990.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.260; most accessible tissue: Minghui63 panicle, score: 98.240 |
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