27 variations found. Os07g0186200/LOC_Os07g08860 (S-domain receptor-like protein kinase; putative; expressed), ranging from 4,593,093 bp to 4,595,607 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g08860 | S-domain receptor-like protein kinase, putative, expressed; RAP ID: Os07g0186200; MSU ID: LOC_Os07g08860 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os07g08860 | Os07g0186200 | OsSIK2 | SIK2 | STRESS INDUCED PROTEIN KINASE 2 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704593163 (J) | chr07 | 4593163 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os07g08860.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 43.735; most accessible tissue: Zhenshan97 panicle, score: 74.671 |
| vg0704593185 (J) | chr07 | 4593185 | C | G | 99.30% | 0.00% | C -> G,T | NA |
LOC_Os07g08860.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 46.031; most accessible tissue: Zhenshan97 panicle, score: 77.482 |
| vg0704593250 (J) | chr07 | 4593250 | A | G | 54.50% | 0.00% | G -> A |
mr1083 (All); LR P-value: 5.48E-24;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 7.69E-12; mr1155 (All); LR P-value: 2.59E-21; mr1195 (All); LR P-value: 4.68E-11; mr1204 (All); LR P-value: 1.34E-30; mr1408 (All); LR P-value: 3.86E-06; mr1436 (All); LR P-value: 4.31E-28; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1578 (All); LR P-value: 9.54E-10; mr1663 (All); LR P-value: 9.86E-10; mr1721 (All); LR P-value: 3.62E-40; mr1819 (All); LR P-value: 2.81E-11; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1916 (All); LR P-value: 5.15E-15; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 47.782; most accessible tissue: Zhenshan97 panicle, score: 76.605 |
| vg0704593311 (J) | chr07 | 4593311 | C | T | 54.20% | 0.00% | T -> C |
mr1083 (All); LR P-value: 1.94E-24;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 6.66E-12; mr1155 (All); LR P-value: 1.33E-21; mr1195 (All); LR P-value: 4.29E-11; mr1204 (All); LR P-value: 9.54E-32; mr1233 (All); LR P-value: 1.79E-11; mr1436 (All); LR P-value: 7.02E-29; mr1560 (All); LR P-value: 8.58E-30; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1578 (All); LR P-value: 1.40E-09; mr1663 (All); LR P-value: 1.83E-09; mr1721 (All); LR P-value: 8.75E-40; mr1819 (All); LR P-value: 6.77E-11; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1916 (All); LR P-value: 4.78E-15; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 54.086; most accessible tissue: Zhenshan97 panicle, score: 79.071 |
| vg0704593347 (J) | chr07 | 4593347 | T | A | 53.50% | 0.34% | A -> T |
mr1083 (All); LR P-value: 7.90E-24;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 2.81E-11; mr1155 (All); LR P-value: 2.80E-21; mr1195 (All); LR P-value: 9.43E-11; mr1204 (All); LR P-value: 5.63E-31; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1793 (All); LR P-value: 1.26E-28; mr1819 (All); LR P-value: 1.33E-10; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 48.761; most accessible tissue: Zhenshan97 panicle, score: 75.670 |
| vg0704593390 (J) | chr07 | 4593390 | C | T | 54.30% | 0.17% | T -> C |
mr1083 (All); LR P-value: 2.95E-24;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 5.35E-12; mr1195 (All); LR P-value: 8.92E-11; mr1204 (All); LR P-value: 4.59E-31; mr1233 (All); LR P-value: 1.76E-11; mr1281 (All); LR P-value: 1.12E-10; mr1436 (All); LR P-value: 2.16E-28; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1578 (All); LR P-value: 2.90E-09; mr1663 (All); LR P-value: 2.69E-09; mr1721 (All); LR P-value: 1.11E-40; mr1819 (All); LR P-value: 9.63E-11; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08860.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 46.801; most accessible tissue: Zhenshan97 young leaf, score: 69.263 |
| vg0704593589 (J) | chr07 | 4593589 | T | C | 99.50% | 0.00% | T -> C | NA |
LOC_Os07g08860.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 51.229; most accessible tissue: Minghui63 panicle, score: 66.554 |
| vg0704593700 (J) | chr07 | 4593700 | T | C | 54.60% | 0.00% | C -> T |
mr1083 (All); LR P-value: 7.66E-24;
mr1083 (Ind_All); LR P-value: 2.25E-06; mr1138 (All); LR P-value: 1.09E-11; mr1155 (All); LR P-value: 2.28E-21; mr1195 (All); LR P-value: 2.49E-11; mr1204 (All); LR P-value: 3.74E-31; mr1436 (All); LR P-value: 2.19E-28; mr1551 (All); LR P-value: 2.96E-24; mr1578 (All); LR P-value: 1.19E-09; mr1663 (All); LR P-value: 6.84E-10; mr1721 (All); LR P-value: 4.53E-40; mr1819 (All); LR P-value: 2.49E-11; mr1860 (Ind_All); LR P-value: 5.48E-06; mr1916 (All); LR P-value: 2.51E-15; mr1707_2 (Ind_All); LR P-value: 2.55E-06 |
LOC_Os07g08860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.917; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0704593720 (J) | chr07 | 4593720 | C | T | 97.60% | 0.00% | C -> T | NA |
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 55.340; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0704593747 (J) | chr07 | 4593747 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 56.741; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0704593763 (J) | chr07 | 4593763 | C | T | 54.20% | 0.21% | T -> C |
mr1083 (All); LR P-value: 3.02E-24;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 1.31E-11; mr1155 (All); LR P-value: 1.55E-21; mr1195 (All); LR P-value: 6.33E-11; mr1204 (All); LR P-value: 2.43E-31; mr1408 (All); LR P-value: 4.47E-06; mr1436 (All); LR P-value: 1.66E-28; mr1560 (All); LR P-value: 1.42E-29; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1578 (All); LR P-value: 3.61E-09; mr1663 (All); LR P-value: 2.57E-09; mr1721 (All); LR P-value: 1.82E-39; mr1819 (All); LR P-value: 9.49E-11; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08860.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 56.124; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0704593805 (J) | chr07 | 4593805 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os07g08860.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 57.775; most accessible tissue: Zhenshan97 panicle, score: 71.253 |
| vg0704593825 (J) | chr07 | 4593825 | C | T | 54.50% | 0.00% | T -> C |
mr1076 (All); LR P-value: 1.18E-25;
mr1083 (All); LR P-value: 4.22E-24; mr1083 (Ind_All); LR P-value: 1.46E-06; mr1107 (Ind_All); LR P-value: 6.67E-06; mr1138 (All); LR P-value: 1.72E-11; mr1155 (All); LR P-value: 4.70E-22; mr1195 (All); LR P-value: 4.35E-11; mr1204 (All); LR P-value: 1.58E-30; mr1233 (All); LR P-value: 3.36E-12; mr1281 (All); LR P-value: 1.04E-10; mr1408 (All); LR P-value: 1.01E-06; mr1436 (All); LR P-value: 4.99E-28; mr1560 (All); LR P-value: 1.40E-29; mr1560 (Ind_All); LR P-value: 2.46E-06; mr1578 (All); LR P-value: 3.21E-09; mr1663 (All); LR P-value: 2.77E-09; mr1721 (All); LR P-value: 4.37E-40; mr1819 (All); LR P-value: 6.84E-11; mr1860 (Ind_All); LR P-value: 6.94E-06; mr1970 (All); LR P-value: 2.56E-62; mr1707_2 (Ind_All); LR P-value: 3.16E-06 |
LOC_Os07g08860.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 58.260; most accessible tissue: Zhenshan97 panicle, score: 73.605 |
| vg0704593842 (J) | chr07 | 4593842 | A | G | 54.20% | 0.32% | G -> A |
mr1083 (All); LR P-value: 2.26E-23;
mr1083 (Ind_All); LR P-value: 1.46E-06; mr1107 (Ind_All); LR P-value: 6.67E-06; mr1138 (All); LR P-value: 3.04E-11; mr1155 (All); LR P-value: 1.94E-21; mr1195 (All); LR P-value: 7.41E-11; mr1204 (All); LR P-value: 9.96E-30; mr1233 (All); LR P-value: 1.38E-11; mr1408 (All); LR P-value: 1.16E-06; mr1560 (Ind_All); LR P-value: 2.46E-06; mr1819 (All); LR P-value: 6.00E-11; mr1860 (Ind_All); LR P-value: 6.94E-06; mr1707_2 (Ind_All); LR P-value: 3.16E-06 |
LOC_Os07g08860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 55.988; most accessible tissue: Zhenshan97 panicle, score: 72.468 |
| vg0704593889 (J) | chr07 | 4593889 | A | G | 99.50% | 0.00% | A -> G | NA |
LOC_Os07g08860.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.248; most accessible tissue: Zhenshan97 panicle, score: 71.253 |
| vg0704594046 (J) | chr07 | 4594046 | A | C | 54.20% | 0.34% | C -> A |
mr1083 (All); LR P-value: 4.83E-24;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 2.21E-11; mr1155 (All); LR P-value: 3.24E-21; mr1195 (All); LR P-value: 2.19E-11; mr1204 (All); LR P-value: 1.57E-31; mr1436 (All); LR P-value: 1.75E-28; mr1551 (All); LR P-value: 5.32E-24; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1578 (All); LR P-value: 1.23E-09; mr1663 (All); LR P-value: 1.20E-09; mr1819 (All); LR P-value: 1.23E-10; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1916 (All); LR P-value: 2.69E-15; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 50.125; most accessible tissue: Callus, score: 62.655 |
| vg0704594123 (J) | chr07 | 4594123 | G | T | 54.00% | 0.00% | T -> G |
mr1083 (All); LR P-value: 3.25E-23;
mr1083 (Ind_All); LR P-value: 9.99E-07; mr1107 (Ind_All); LR P-value: 9.66E-06; mr1138 (All); LR P-value: 3.11E-11; mr1195 (All); LR P-value: 5.01E-11; mr1204 (All); LR P-value: 1.19E-29; mr1281 (All); LR P-value: 9.68E-11; mr1316 (All); LR P-value: 2.78E-10; mr1551 (All); LR P-value: 2.14E-24; mr1560 (Ind_All); LR P-value: 5.02E-06; mr1578 (All); LR P-value: 1.21E-09; mr1663 (All); LR P-value: 8.39E-10; mr1793 (All); LR P-value: 4.98E-28; mr1819 (All); LR P-value: 3.87E-11; mr1836 (All); LR P-value: 2.89E-07; mr1860 (Ind_All); LR P-value: 5.10E-06; mr1916 (All); LR P-value: 3.60E-15; mr1707_2 (Ind_All); LR P-value: 2.14E-06 |
LOC_Os07g08860.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 46.367; most accessible tissue: Zhenshan97 panicle, score: 57.341 |
| vg0704594140 (J) | chr07 | 4594140 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os07g08860.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08850.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08870.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.903; most accessible tissue: Zhenshan97 panicle, score: 59.590 |
| vg0704594218 (J) | chr07 | 4594218 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os07g08860.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08850.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08870.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.191; most accessible tissue: Callus, score: 67.415 |
| vg0704594273 (J) | chr07 | 4594273 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os07g08860.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os07g08850.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08870.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.272; most accessible tissue: Callus, score: 67.415 |
| vg0704594356 (J) | chr07 | 4594356 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g08850.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08870.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.477; most accessible tissue: Zhenshan97 young leaf, score: 63.653 |
| vg0704594483 (J) | chr07 | 4594483 | A | G | 98.50% | 0.00% | A -> G | NA |
LOC_Os07g08860.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.313; most accessible tissue: Zhenshan97 young leaf, score: 70.177 |
| vg0704594515 (J) | chr07 | 4594515 | C | T | 87.50% | 0.00% | C -> T |
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 64.493; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
|
| vg0704595098 (J) | chr07 | 4595098 | A | G | 98.50% | 0.00% | A -> G | NA |
LOC_Os07g08860.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.418; most accessible tissue: Zhenshan97 young leaf, score: 80.589 |
| vg0704595308 (J) | chr07 | 4595308 | CCTAG | C | 55.50% | 0.02% | C -> CCTAG | NA |
LOC_Os07g08860.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08860.1 Alt: CCTAG| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 71.188; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
| vg0704595447 (J) | chr07 | 4595447 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os07g08860.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g08850.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08870.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.222; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
| vg0704595469 (J) | chr07 | 4595469 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os07g08860.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g08850.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08870.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.867; most accessible tissue: Zhenshan97 panicle, score: 86.432 |