10 variations found. Os01g0695900/LOC_Os01g50110 (MYB family transcription factor; putative; expressed), ranging from 28,796,515 bp to 28,797,732 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g50110 | MYB family transcription factor, putative, expressed; RAP ID: Os01g0695900; MSU ID: LOC_Os01g50110 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os01g50110 | Os01g0695900 | OsMyb4, OSMYB4, MYB4 | myb transcription factor 4, transcription factor MYB4 | D88620. | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128796617 (J) | chr01 | 28796617 | G | A | 98.80% | 0.00% | G -> A | NA |
LOC_Os01g50110.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.216; most accessible tissue: Zhenshan97 flower, score: 91.578 |
| vg0128796715 (J) | chr01 | 28796715 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os01g50110.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g50100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.042; most accessible tissue: Zhenshan97 flower, score: 88.191 |
| vg0128796758 (J) | chr01 | 28796758 | G | T | 99.20% | 0.00% | G -> T,A,C | NA |
LOC_Os01g50110.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g50100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50110.1 Alt: A| synonymous_variant LOW(snpEff) LOC_Os01g50100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50110.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os01g50100.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.760; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0128796905 (J) | chr01 | 28796905 | C | G | 97.10% | 0.00% | C -> G | NA |
LOC_Os01g50100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50120.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50110.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.595; most accessible tissue: Minghui63 young leaf, score: 86.554 |
| vg0128797210 (J) | chr01 | 28797210 | T | C | 60.50% | 0.00% | C -> T |
mr1053 (All); LR P-value: 8.58E-07;
mr1089 (All); LR P-value: 1.82E-43; mr1104 (All); LR P-value: 6.60E-35; mr1125 (All); LR P-value: 1.25E-47; mr1129 (All); LR P-value: 1.04E-35; mr1147 (All); LR P-value: 2.59E-17; mr1208 (All); LR P-value: 2.05E-30; mr1213 (All); LR P-value: 9.76E-32; mr1225 (All); LR P-value: 6.12E-31; mr1233 (All); LR P-value: 4.52E-12; mr1251 (All); LR P-value: 2.48E-25; mr1253 (All); LR P-value: 3.74E-18; mr1257 (All); LR P-value: 5.98E-32; mr1260 (All); LR P-value: 8.34E-09; mr1411 (All); LR P-value: 9.42E-25; mr1745 (All); LR P-value: 1.29E-35; mr1748 (All); LR P-value: 2.94E-06; mr1763 (All); LR P-value: 3.47E-07; mr1805 (Jap_All); LR P-value: 8.46E-07; mr1807 (All); LR P-value: 1.77E-19; mr1129_2 (All); LR P-value: 8.84E-36; mr1228_2 (All); LR P-value: 1.64E-11; mr1253_2 (All); LR P-value: 7.50E-21; mr1401_2 (All); LR P-value: 1.88E-24; mr1527_2 (All); LR P-value: 1.17E-07; mr1745_2 (All); LR P-value: 1.18E-42; mr1807_2 (All); LR P-value: 1.06E-15 |
LOC_Os01g50110.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.268; most accessible tissue: Minghui63 young leaf, score: 81.195 |
| vg0128797257 (J) | chr01 | 28797257 | G | A | 97.10% | 0.00% | G -> A | NA |
LOC_Os01g50110.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.315; most accessible tissue: Zhenshan97 young leaf, score: 81.353 |
| vg0128797534 (J) | chr01 | 28797534 | G | T | 98.80% | 0.00% | G -> T | NA |
LOC_Os01g50110.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g50100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g50120.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.647; most accessible tissue: Callus, score: 86.238 |
| vg0128797626 (J) | chr01 | 28797626 | C | G | 70.80% | 0.00% | G -> C |
mr1241 (All); LR P-value: 7.54E-52;
mr1334 (All); LR P-value: 3.15E-87; mr1486 (All); LR P-value: 7.65E-37; mr1548 (All); LR P-value: 9.29E-23; mr1805 (All); LR P-value: 8.69E-26; mr1277_2 (All); LR P-value: 1.92E-14; mr1334_2 (All); LR P-value: 8.79E-99; mr1486_2 (All); LR P-value: 4.52E-44; mr1682_2 (All); LR P-value: 7.91E-18; mr1698_2 (All); LR P-value: 4.24E-21; mr1730_2 (All); LR P-value: 9.50E-17; mr1805_2 (All); LR P-value: 5.40E-44; mr1866_2 (All); LR P-value: 4.54E-15; mr1991_2 (All); LR P-value: 3.31E-55 |
LOC_Os01g50110.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50100.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.045; most accessible tissue: Zhenshan97 young leaf, score: 81.600 |
| vg0128797631 (J) | chr01 | 28797631 | A | G | 60.30% | 0.00% | G -> A |
mr1089 (All); LR P-value: 3.22E-43;
mr1104 (All); LR P-value: 3.33E-34; mr1129 (All); LR P-value: 2.70E-35; mr1147 (All); LR P-value: 4.64E-17; mr1208 (All); LR P-value: 6.65E-30; mr1225 (All); LR P-value: 1.47E-30; mr1233 (All); LR P-value: 1.29E-11; mr1251 (All); LR P-value: 9.39E-26; mr1253 (All); LR P-value: 9.37E-19; mr1257 (All); LR P-value: 9.33E-32; mr1260 (All); LR P-value: 7.72E-09; mr1745 (All); LR P-value: 2.86E-35; mr1748 (All); LR P-value: 2.45E-06; mr1763 (All); LR P-value: 4.90E-07; mr1805 (Jap_All); LR P-value: 8.46E-07; mr1807 (All); LR P-value: 6.11E-19; mr1228_2 (All); LR P-value: 5.19E-12; mr1401_2 (All); LR P-value: 8.79E-25; mr1527_2 (All); LR P-value: 6.49E-08; mr1745_2 (All); LR P-value: 4.75E-42; mr1807_2 (All); LR P-value: 6.62E-16 |
LOC_Os01g50110.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.978; most accessible tissue: Zhenshan97 young leaf, score: 81.353 |
| vg0128797659 (J) | chr01 | 28797659 | G | A | 70.80% | 0.00% | A -> G |
mr1334 (All); LR P-value: 8.49E-86;
mr1486 (All); LR P-value: 3.47E-36; mr1548 (All); LR P-value: 3.63E-22; mr1690 (All); LR P-value: 8.75E-07; mr1805 (All); LR P-value: 1.91E-25; mr1334_2 (All); LR P-value: 1.34E-97; mr1682_2 (All); LR P-value: 6.28E-18; mr1698_2 (All); LR P-value: 3.06E-21; mr1730_2 (All); LR P-value: 3.43E-17; mr1805_2 (All); LR P-value: 4.66E-43; mr1866_2 (All); LR P-value: 1.95E-15; mr1991_2 (All); LR P-value: 6.35E-55 |
LOC_Os01g50110.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g50120.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.424; most accessible tissue: Zhenshan97 young leaf, score: 80.325 |