15 variations found. Os03g0327600/LOC_Os03g21040 (stress responsive protein; putative; expressed), ranging from 11,957,260 bp to 11,959,777 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g21040 | stress responsive protein, putative, expressed; RAP ID: Os03g0327600; MSU ID: LOC_Os03g21040 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0311957618 (J) | chr03 | 11957618 | A | T | 63.60% | 0.25% | T -> A | NA |
LOC_Os03g21040.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.951; most accessible tissue: Zhenshan97 panicle, score: 98.397 |
| vg0311957642 (J) | chr03 | 11957642 | ATCG | A | 98.90% | 0.00% | ATCG -> A | NA |
LOC_Os03g21040.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.819; most accessible tissue: Zhenshan97 panicle, score: 98.324 |
| vg0311957786 (J) | chr03 | 11957786 | C | T | 63.50% | 0.28% | T -> C | NA |
LOC_Os03g21040.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 88.320; most accessible tissue: Zhenshan97 panicle, score: 97.598 |
| vg0311957847 (J) | chr03 | 11957847 | C | G | 63.60% | 0.23% | G -> C | NA |
LOC_Os03g21040.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.948; most accessible tissue: Zhenshan97 panicle, score: 97.353 |
| vg0311957911 (J) | chr03 | 11957911 | CA | C | 99.70% | 0.00% | CA -> C | NA |
LOC_Os03g21040.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g21050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g21040.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.507; most accessible tissue: Zhenshan97 panicle, score: 97.490 |
| vg0311957930 (J) | chr03 | 11957930 | C | A | 63.50% | 0.28% | A -> C | NA |
LOC_Os03g21040.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.614; most accessible tissue: Zhenshan97 panicle, score: 97.422 |
| vg0311958624 (J) | chr03 | 11958624 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g21040.2 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g21040.3 Alt: A| synonymous_variant LOW(snpEff) LOC_Os03g21050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.579; most accessible tissue: Zhenshan97 panicle, score: 98.100 |
| vg0311958639 (J) | chr03 | 11958639 | C | G | 63.50% | 0.28% | G -> C | NA |
LOC_Os03g21040.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g21040.3 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g21040.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g21040.3 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.820; most accessible tissue: Zhenshan97 panicle, score: 98.115 |
| vg0311958984 (J) | chr03 | 11958984 | A | G | 63.50% | 0.28% | G -> A | NA |
LOC_Os03g21040.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g21040.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g21040.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g21040.3 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.357; most accessible tissue: Zhenshan97 panicle, score: 98.719 |
| vg0311959145 (J) | chr03 | 11959145 | A | G | 63.50% | 0.28% | G -> A | NA |
LOC_Os03g21050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21040.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 88.855; most accessible tissue: Zhenshan97 panicle, score: 99.024 |
| vg0311959499 (J) | chr03 | 11959499 | G | T | 58.70% | 0.25% | T -> G |
mr1063 (All); LR P-value: 7.96E-49;
mr1064 (All); LR P-value: 4.02E-36; mr1164 (All); LR P-value: 6.21E-15; mr1246 (All); LR P-value: 1.17E-60; mr1580 (All); LR P-value: 6.68E-20; mr1825 (All); LR P-value: 2.21E-17; mr1913 (All); LR P-value: 8.15E-18; mr1943 (All); LR P-value: 8.32E-23; mr1970 (All); LR P-value: 4.75E-63; mr1973 (All); LR P-value: 3.55E-83; mr1037_2 (All); LR P-value: 1.71E-30; mr1325_2 (All); LR P-value: 1.48E-12; mr1350_2 (All); LR P-value: 1.44E-23; mr1386_2 (All); LR P-value: 6.16E-23; mr1571_2 (All); LR P-value: 2.27E-32; mr1745_2 (All); LR P-value: 9.62E-39; mr1793_2 (All); LR P-value: 9.83E-46; mr1970_2 (All); LR P-value: 1.50E-63; mr1973_2 (All); LR P-value: 1.89E-101 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g21040.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21050.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.280; most accessible tissue: Zhenshan97 panicle, score: 99.790 |
| vg0311959649 (J) | chr03 | 11959649 | GA | G | 95.20% | 0.00% | GA -> G,GAA | NA |
LOC_Os03g21040.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.2 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21050.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.507; most accessible tissue: Zhenshan97 panicle, score: 99.846 |
| vg0311959678 (J) | chr03 | 11959678 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os03g21040.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g21050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g21040.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.795; most accessible tissue: Zhenshan97 panicle, score: 99.828 |
| vg0311959727 (J) | chr03 | 11959727 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os03g21040.2 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g21050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g21040.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.243; most accessible tissue: Zhenshan97 panicle, score: 99.772 |
| STR0311959135 (J) | chr03 | 11959135 | CGACGGC GACA | CGACGGC GACG | 63.30% | 0.00% | CGACGGCGAC G -> CGACGGCGAC A | NA |
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