59 variations found. Os03g0839900/LOC_Os03g62340 (protein kinase family protein; putative; expressed), ranging from 35,312,450 bp to 35,317,359 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g62340 | protein kinase family protein, putative, expressed; RAP ID: Os03g0839900; MSU ID: LOC_Os03g62340 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0335312937 (J) | chr03 | 35312937 | CAGCAGC AGCA | CAGCAGC AGCAGCA | 58.70% | 0.00% | CAGCAGCAGC A -> CAGCAGCAGC AGCA | NA |
|
| vg0335312587 (J) | chr03 | 35312587 | T | G | 99.80% | 0.00% | T -> G | NA |
LOC_Os03g62340.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.851; most accessible tissue: Zhenshan97 flower, score: 97.841 |
| vg0335312625 (J) | chr03 | 35312625 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g62340.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.794; most accessible tissue: Zhenshan97 flower, score: 97.953 |
| vg0335312849 (J) | chr03 | 35312849 | A | T | 95.70% | 0.00% | A -> T | NA |
LOC_Os03g62340.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.569; most accessible tissue: Zhenshan97 flower, score: 95.918 |
| vg0335312932 (J) | chr03 | 35312932 | C | CACA | 59.80% | 0.06% | C -> CACA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g62340.1 Alt: CACA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62314.1 Alt: CACA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: CACA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.672; most accessible tissue: Zhenshan97 flower, score: 96.028 |
| vg0335312943 (J) | chr03 | 35312943 | C | Unkown | 97.90% | 0.78% | C -> T | NA |
LOC_Os03g62340.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.562; most accessible tissue: Zhenshan97 flower, score: 96.097 |
| vg0335312945 (J) | chr03 | 35312945 | G | A | 88.00% | 0.00% | G -> A | NA |
LOC_Os03g62340.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.547; most accessible tissue: Zhenshan97 flower, score: 96.097 |
| vg0335312979 (J) | chr03 | 35312979 | C | T | 64.40% | 0.02% | C -> T | NA |
LOC_Os03g62340.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.919; most accessible tissue: Zhenshan97 flower, score: 96.415 |
| vg0335313112 (J) | chr03 | 35313112 | C | A | 60.60% | 0.00% | C -> A |
LOC_Os03g62340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.004; most accessible tissue: Zhenshan97 flower, score: 94.897 |
|
| vg0335313293 (J) | chr03 | 35313293 | T | C | 96.60% | 0.00% | T -> C | NA |
LOC_Os03g62314.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.193; most accessible tissue: Zhenshan97 flower, score: 94.709 |
| vg0335313372 (J) | chr03 | 35313372 | G | A | 99.00% | 0.00% | G -> A,T | NA |
LOC_Os03g62340.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g62314.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: A| synonymous_variant LOW(snpEff) LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.945; most accessible tissue: Zhenshan97 flower, score: 93.469 |
| vg0335313374 (J) | chr03 | 35313374 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os03g62340.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.222; most accessible tissue: Zhenshan97 flower, score: 93.634 |
| vg0335313411 (J) | chr03 | 35313411 | T | A | 99.80% | 0.00% | T -> A,G | NA |
LOC_Os03g62340.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: G| synonymous_variant LOW(snpEff) LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.351; most accessible tissue: Zhenshan97 flower, score: 93.614 |
| vg0335313569 (J) | chr03 | 35313569 | A | G | 82.60% | 0.00% | G -> A |
mr1115 (All); LR P-value: 4.79E-22;
mr1137 (All); LR P-value: 1.29E-30; mr1606 (All); LR P-value: 3.23E-07; mr1611 (All); LR P-value: 2.70E-22; mr1866 (All); LR P-value: 1.01E-09; mr1920 (All); LR P-value: 1.22E-21; mr1115_2 (All); LR P-value: 7.09E-27; mr1137_2 (All); LR P-value: 1.65E-37; mr1180_2 (Jap_All); LR P-value: 5.38E-07; mr1183_2 (Jap_All); LR P-value: 7.66E-07; mr1554_2 (Jap_All); LR P-value: 9.52E-07; mr1611_2 (All); LR P-value: 1.82E-22; mr1617_2 (All); LR P-value: 8.16E-27; mr1730_2 (All); LR P-value: 1.51E-16; mr1730_2 (Jap_All); LR P-value: 2.77E-06; mr1794_2 (Jap_All); LR P-value: 2.69E-08 |
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g62340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.176; most accessible tissue: Zhenshan97 flag leaf, score: 94.800 |
| vg0335313627 (J) | chr03 | 35313627 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os03g62314.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g62330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.123; most accessible tissue: Zhenshan97 flag leaf, score: 94.083 |
| vg0335313857 (J) | chr03 | 35313857 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os03g62340.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.562; most accessible tissue: Zhenshan97 flag leaf, score: 91.771 |
| vg0335313869 (J) | chr03 | 35313869 | G | A | 95.70% | 0.00% | G -> A | NA |
LOC_Os03g62340.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.380; most accessible tissue: Zhenshan97 flag leaf, score: 91.729 |
| vg0335313935 (J) | chr03 | 35313935 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62340.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.765; most accessible tissue: Zhenshan97 flower, score: 86.488 |
| vg0335313972 (J) | chr03 | 35313972 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os03g62340.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g62314.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g62330.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.886; most accessible tissue: Zhenshan97 flower, score: 83.915 |
| vg0335314343 (J) | chr03 | 35314343 | T | A | 57.90% | 0.00% | T -> A |
mr1606 (Jap_All); LR P-value: 5.26E-06;
mr1942 (All); LR P-value: 4.65E-09; mr1168_2 (Ind_All); LR P-value: 1.55E-06; mr1183_2 (Jap_All); LR P-value: 1.20E-06; mr1338_2 (Jap_All); LR P-value: 2.54E-07; mr1383_2 (Jap_All); LR P-value: 6.46E-06; mr1607_2 (All); LR P-value: 3.14E-08; mr1794_2 (Jap_All); LR P-value: 1.23E-07; mr1815_2 (All); LR P-value: 1.53E-06; mr1942_2 (All); LR P-value: 2.58E-11 |
LOC_Os03g62340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 63.393; most accessible tissue: Minghui63 young leaf, score: 78.443 |
| vg0335314427 (J) | chr03 | 35314427 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g62330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g62340.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.399; most accessible tissue: Minghui63 young leaf, score: 79.549 |
| vg0335314709 (J) | chr03 | 35314709 | T | C | 59.70% | 0.00% | T -> C | NA |
LOC_Os03g62340.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.601; most accessible tissue: Callus, score: 78.573 |
| vg0335314719 (J) | chr03 | 35314719 | T | A | 88.80% | 0.00% | T -> A | NA |
LOC_Os03g62340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 62.603; most accessible tissue: Callus, score: 78.573 |
| vg0335314920 (J) | chr03 | 35314920 | G | A | 76.40% | 0.08% | G -> A | NA |
LOC_Os03g62340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g62340.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 55.547; most accessible tissue: Zhenshan97 panicle, score: 73.605 |
| vg0335315030 (J) | chr03 | 35315030 | A | G | 96.50% | 0.00% | A -> G | NA |
LOC_Os03g62340.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.372; most accessible tissue: Callus, score: 79.403 |
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