12 variations found. Os03g0113000/LOC_Os03g02190 (protein kinase domain containing protein; expressed), ranging from 732,485 bp to 734,247 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g02190 | protein kinase domain containing protein, expressed; RAP ID: Os03g0113000; MSU ID: LOC_Os03g02190 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0300732581 (J) | chr03 | 732581 | G | A | 93.10% | 0.00% | G -> A |
LOC_Os03g02190.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g02180.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0300732789 (J) | chr03 | 732789 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os03g02190.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g02180.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300732800 (J) | chr03 | 732800 | A | AAATTGA G | 93.10% | 0.00% | A -> AAATTGAG,A AATTAAG | NA |
LOC_Os03g02190.1 Alt: AAATTAAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g02180.1 Alt: AAATTAAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.1 Alt: AAATTAAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.2 Alt: AAATTAAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.3 Alt: AAATTAAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02190.1 Alt: AAATTGAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02180.1 Alt: AAATTGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.1 Alt: AAATTGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.2 Alt: AAATTGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.3 Alt: AAATTGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300732801 (J) | chr03 | 732801 | C | CTGCTTT TTT | 93.10% | 0.00% | C -> CTGCTTTTTT | NA |
LOC_Os03g02190.1 Alt: CTGCTTTTTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g02180.1 Alt: CTGCTTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.1 Alt: CTGCTTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.2 Alt: CTGCTTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.3 Alt: CTGCTTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300732841 (J) | chr03 | 732841 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os03g02190.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g02180.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300732874 (J) | chr03 | 732874 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os03g02190.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g02180.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300732994 (J) | chr03 | 732994 | T | C | 54.70% | 0.00% | C -> T |
mr1191 (All); LR P-value: 2.68E-09;
mr1317 (All); LR P-value: 4.72E-09; mr1317 (Ind_All); LR P-value: 7.83E-08; mr1607 (Ind_All); LR P-value: 5.64E-06; mr1644 (All); LR P-value: 1.56E-09; mr1818 (Ind_All); LR P-value: 1.09E-07; mr1855 (Ind_All); LR P-value: 6.95E-11; mr1877 (Ind_All); LR P-value: 2.38E-07; mr1918 (Ind_All); LR P-value: 7.63E-06; mr1050_2 (All); LR P-value: 5.29E-09; mr1050_2 (Ind_All); LR P-value: 8.54E-06; mr1191_2 (All); LR P-value: 3.15E-15; mr1317_2 (Ind_All); LR P-value: 2.19E-08; mr1321_2 (All); LR P-value: 2.12E-07; mr1428_2 (Ind_All); LR P-value: 2.79E-06; mr1446_2 (All); LR P-value: 3.69E-08; mr1818_2 (Ind_All); LR P-value: 6.51E-06; mr1875_2 (All); LR P-value: 1.10E-06; mr1914_2 (Ind_All); LR P-value: 3.62E-07; mr1946_2 (All); LR P-value: 3.39E-09; mr1948_2 (All); LR P-value: 3.39E-09 |
LOC_Os03g02190.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g02180.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g02200.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300733085 (J) | chr03 | 733085 | G | T | 98.80% | 0.00% | G -> T | NA |
LOC_Os03g02190.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g02200.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300733603 (J) | chr03 | 733603 | C | A | 97.10% | 0.00% | C -> A | NA |
LOC_Os03g02190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300733892 (J) | chr03 | 733892 | A | G | 54.60% | 0.28% | G -> A,C |
mr1317 (All); LR P-value: 4.91E-09;
mr1317 (Ind_All); LR P-value: 2.17E-07; mr1607 (Ind_All); LR P-value: 3.42E-06; mr1644 (All); LR P-value: 5.47E-09; mr1818 (Ind_All); LR P-value: 1.80E-08; mr1855 (Ind_All); LR P-value: 6.95E-11; mr1877 (Ind_All); LR P-value: 1.98E-07; mr1050_2 (All); LR P-value: 1.18E-09; mr1050_2 (Ind_All); LR P-value: 2.05E-06; mr1191_2 (All); LR P-value: 2.30E-14; mr1272_2 (All); LR P-value: 2.40E-06; mr1317_2 (Ind_All); LR P-value: 4.68E-08; mr1321_2 (All); LR P-value: 9.61E-08; mr1428_2 (Ind_All); LR P-value: 1.39E-06; mr1446_2 (All); LR P-value: 3.18E-08; mr1855_2 (Ind_All); LR P-value: 6.76E-07; mr1875_2 (All); LR P-value: 1.84E-06; mr1914_2 (Ind_All); LR P-value: 4.48E-07; mr1946_2 (All); LR P-value: 7.15E-09; mr1948_2 (All); LR P-value: 7.15E-09 |
LOC_Os03g02190.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os03g02200.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g02190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300734013 (J) | chr03 | 734013 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os03g02190.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g02200.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0300734181 (J) | chr03 | 734181 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os03g02190.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os03g02190.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g02200.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g02200.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |