34 variations found. Os02g0787300/LOC_Os02g54600 (STE_MEK_ste7_MAP2K.5 - STE kinases include homologs to sterile 7; sterile 11 and sterile 20 from yeast; expressed), ranging from 33,442,068 bp to 33,443,948 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g54600 | STE_MEK_ste7_MAP2K.5 - STE kinases include homologs to sterile 7, sterile 11 and sterile 20 from yeast, expressed; RAP ID: Os02g0787300; MSU ID: LOC_Os02g54600 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os02g54600 | Os02g0787300 | OsMKK4 | MAPK kinase 4 | DQ848674. Gene Expression Omnibus database: GSE15613. | MKK4 | MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233442116 (J) | chr02 | 33442116 | C | T | 98.10% | 0.00% | C -> T | NA |
LOC_Os02g54600.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.977; most accessible tissue: Minghui63 flower, score: 99.201 |
| vg0233442119 (J) | chr02 | 33442119 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os02g54600.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.981; most accessible tissue: Minghui63 flower, score: 99.201 |
| vg0233442136 (J) | chr02 | 33442136 | A | G | 60.40% | 0.00% | G -> A |
mr1097 (All); LR P-value: 2.58E-09;
mr1102 (All); LR P-value: 2.77E-21; mr1134 (All); LR P-value: 2.45E-80; mr1146 (All); LR P-value: 5.59E-15; mr1148 (All); LR P-value: 5.18E-27; mr1152 (All); LR P-value: 2.77E-44; mr1194 (All); LR P-value: 3.13E-43; mr1278 (All); LR P-value: 1.31E-06; mr1350 (All); LR P-value: 1.12E-34; mr1579 (All); LR P-value: 5.46E-12; mr1645 (All); LR P-value: 9.02E-40; mr1647 (All); LR P-value: 6.16E-33; mr1653 (All); LR P-value: 7.28E-14; mr1682 (All); LR P-value: 1.52E-37; mr1686 (All); LR P-value: 4.82E-27; mr1695 (All); LR P-value: 6.18E-59; mr1711 (All); LR P-value: 4.74E-59; mr1723 (All); LR P-value: 2.62E-27; mr1754 (All); LR P-value: 1.54E-19; mr1767 (All); LR P-value: 1.18E-17; mr1979 (All); LR P-value: 9.00E-07; mr1097_2 (All); LR P-value: 1.64E-11; mr1146_2 (All); LR P-value: 9.04E-17; mr1150_2 (All); LR P-value: 1.10E-32; mr1223_2 (All); LR P-value: 6.36E-35; mr1239_2 (All); LR P-value: 5.21E-19; mr1893_2 (All); LR P-value: 1.64E-10 |
LOC_Os02g54600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.021; most accessible tissue: Minghui63 flower, score: 99.191 |
| vg0233442142 (J) | chr02 | 33442142 | G | GGAA | 53.90% | 0.00% | GGAA -> G | NA |
LOC_Os02g54600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.172; most accessible tissue: Minghui63 flower, score: 99.224 |
| vg0233442145 (J) | chr02 | 33442145 | A | G | 92.50% | 0.00% | A -> G,AGAG,AG |
mr1102 (All); LR P-value: 1.62E-20;
mr1146 (All); LR P-value: 3.88E-15; mr1152 (All); LR P-value: 2.10E-43; mr1333 (All); LR P-value: 2.51E-29; mr1350 (All); LR P-value: 8.55E-35; mr1553 (All); LR P-value: 5.02E-11; mr1646 (All); LR P-value: 3.77E-06; mr1647 (All); LR P-value: 5.50E-32; mr1682 (All); LR P-value: 9.31E-36; mr1686 (All); LR P-value: 4.77E-27; mr1695 (All); LR P-value: 2.40E-58; mr1781 (All); LR P-value: 1.00E-06; mr1917 (All); LR P-value: 1.46E-23; mr1146_2 (All); LR P-value: 1.14E-16; mr1150_2 (All); LR P-value: 1.21E-32; mr1239_2 (All); LR P-value: 2.89E-19; mr1242_2 (All); LR P-value: 1.48E-22; mr1893_2 (All); LR P-value: 1.66E-10 |
LOC_Os02g54600.1 Alt: AGAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: AGAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54600.1 Alt: AG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54590.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.285; most accessible tissue: Minghui63 flower, score: 99.263 |
| vg0233442164 (J) | chr02 | 33442164 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os02g54600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.656; most accessible tissue: Minghui63 flower, score: 98.991 |
| vg0233442208 (J) | chr02 | 33442208 | C | T | 90.50% | 0.00% | T -> C |
LOC_Os02g54600.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.060; most accessible tissue: Minghui63 flower, score: 98.878 |
|
| vg0233442235 (J) | chr02 | 33442235 | CA | C | 60.40% | 0.00% | C -> CA,CAATCCA | NA |
LOC_Os02g54600.1 Alt: CAATCCA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: CAATCCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54600.1 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54590.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.016; most accessible tissue: Minghui63 flower, score: 98.850 |
| vg0233442236 (J) | chr02 | 33442236 | A | AC | 35.90% | 59.06% | A -> AC | NA |
LOC_Os02g54600.1 Alt: AC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.959; most accessible tissue: Minghui63 flower, score: 98.818 |
| vg0233442306 (J) | chr02 | 33442306 | T | TCTC | 51.00% | 0.04% | TCTC -> T | NA |
LOC_Os02g54600.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 94.973; most accessible tissue: Minghui63 flower, score: 98.173 |
| vg0233442402 (J) | chr02 | 33442402 | C | T | 60.30% | 0.00% | T -> C | NA |
LOC_Os02g54600.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.912; most accessible tissue: Minghui63 flower, score: 98.562 |
| vg0233442403 (J) | chr02 | 33442403 | T | C | 97.80% | 0.00% | T -> C | NA |
LOC_Os02g54600.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.845; most accessible tissue: Minghui63 flower, score: 98.515 |
| vg0233442487 (J) | chr02 | 33442487 | A | G | 45.70% | 42.76% | A -> G | NA |
LOC_Os02g54600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 94.615; most accessible tissue: Minghui63 flower, score: 98.224 |
| vg0233442491 (J) | chr02 | 33442491 | AAGAAG | A | 82.40% | 2.69% | AAGAAG -> A,AAAG | NA |
LOC_Os02g54600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54600.1 Alt: AAAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54590.1 Alt: AAAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 94.783; most accessible tissue: Minghui63 flower, score: 98.285 |
| vg0233442492 (J) | chr02 | 33442492 | A | AGAAG | 49.70% | 0.00% | AGAAG -> A,AAAG | NA |
LOC_Os02g54600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54600.1 Alt: AAAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54590.1 Alt: AAAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.812; most accessible tissue: Minghui63 flower, score: 98.285 |
| vg0233442494 (J) | chr02 | 33442494 | AAG | A | 96.30% | 0.74% | AAG -> A | NA |
LOC_Os02g54600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 94.787; most accessible tissue: Minghui63 flower, score: 98.273 |
| vg0233442495 (J) | chr02 | 33442495 | AG | A | 99.70% | 0.00% | AG -> A | NA |
LOC_Os02g54600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.787; most accessible tissue: Minghui63 flower, score: 98.273 |
| vg0233442544 (J) | chr02 | 33442544 | A | G | 97.80% | 0.00% | A -> G | NA |
LOC_Os02g54600.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.969; most accessible tissue: Minghui63 young leaf, score: 97.942 |
| vg0233442570 (J) | chr02 | 33442570 | A | G | 61.30% | 0.00% | G -> A | NA |
LOC_Os02g54600.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.801; most accessible tissue: Minghui63 young leaf, score: 98.094 |
| vg0233442617 (J) | chr02 | 33442617 | T | C | 94.10% | 0.00% | T -> C | NA |
LOC_Os02g54600.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.807; most accessible tissue: Minghui63 young leaf, score: 98.337 |
| vg0233443032 (J) | chr02 | 33443032 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g54600.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g54590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.724; most accessible tissue: Minghui63 young leaf, score: 99.003 |
| vg0233443116 (J) | chr02 | 33443116 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g54600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.483; most accessible tissue: Minghui63 young leaf, score: 98.943 |
| vg0233443158 (J) | chr02 | 33443158 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os02g54600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.534; most accessible tissue: Minghui63 young leaf, score: 98.943 |
| vg0233443176 (J) | chr02 | 33443176 | G | A | 99.30% | 0.00% | G -> A,C | NA |
LOC_Os02g54600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g54600.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os02g54590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.033; most accessible tissue: Minghui63 young leaf, score: 98.943 |
| vg0233443314 (J) | chr02 | 33443314 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g54600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.283; most accessible tissue: Minghui63 young leaf, score: 98.932 |
| vg0233443473 (J) | chr02 | 33443473 | C | A | 94.10% | 0.00% | C -> A | NA |
LOC_Os02g54600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.203; most accessible tissue: Minghui63 flower, score: 98.866 |
| vg0233443542 (J) | chr02 | 33443542 | C | T | 97.20% | 0.00% | C -> T | NA |
LOC_Os02g54600.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.097; most accessible tissue: Minghui63 young leaf, score: 98.816 |
| vg0233443766 (J) | chr02 | 33443766 | T | G | 73.20% | 9.86% | T -> G | NA |
LOC_Os02g54600.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g54600.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 96.489; most accessible tissue: Minghui63 young leaf, score: 99.232 |
| vg0233443771 (J) | chr02 | 33443771 | G | A | 73.50% | 9.67% | G -> A | NA |
LOC_Os02g54600.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g54600.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 96.550; most accessible tissue: Minghui63 young leaf, score: 99.262 |
| vg0233443773 (J) | chr02 | 33443773 | C | T | 73.50% | 9.59% | C -> T | NA |
LOC_Os02g54600.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g54600.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 96.559; most accessible tissue: Minghui63 young leaf, score: 99.265 |
| vg0233443780 (J) | chr02 | 33443780 | GGCTGCT GCT | G | 79.90% | 6.14% | GGCTGCTGCT -> G | NA |
LOC_Os02g54600.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g54600.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 96.552; most accessible tissue: Minghui63 young leaf, score: 99.271 |
| vg0233443801 (J) | chr02 | 33443801 | A | T | 56.70% | 0.87% | T -> A,TGCA | NA |
LOC_Os02g54600.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g54600.1 Alt: TGCA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os02g54600.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 96.502; most accessible tissue: Minghui63 young leaf, score: 99.257 |
| vg0233443892 (J) | chr02 | 33443892 | T | C | 90.10% | 0.76% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g54600.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.309; most accessible tissue: Minghui63 young leaf, score: 99.328 |
| STR0233442610 (J) | chr02 | 33442610 | GTGGTGG T | GTGGTGG C | 96.80% | 0.00% | GTGGTGGT -> GTGGTGGC | NA |
|