9 variations found. Os02g0832150/LOC_Os02g58540 (RING-H2 finger protein; putative; expressed), ranging from 35,783,283 bp to 35,784,146 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g58540 | RING-H2 finger protein, putative, expressed; RAP ID: Os02g0832150; MSU ID: LOC_Os02g58540 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0235783402 (J) | chr02 | 35783402 | G | A | 98.80% | 0.00% | G -> A | NA |
LOC_Os02g58540.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.868; most accessible tissue: Minghui63 flower, score: 85.758 |
| vg0235783514 (J) | chr02 | 35783514 | G | GGGCGGT GGCGGT | 57.90% | 0.00% | GGGCGGTGGC GGT -> G | NA |
LOC_Os02g58540.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 87.426; most accessible tissue: Callus, score: 93.514 |
| vg0235783638 (J) | chr02 | 35783638 | GCAGGTG GCGTGGG TCCCCAG C | G | 99.90% | 0.00% | GCAGGTGGCG TGGGTCCCCA GC -> G | NA |
LOC_Os02g58540.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os02g58530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.303; most accessible tissue: Zhenshan97 panicle, score: 93.133 |
| vg0235783760 (J) | chr02 | 35783760 | C | CCTG | 88.30% | 0.00% | CCTG -> C | NA |
LOC_Os02g58540.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 93.227; most accessible tissue: Zhenshan97 panicle, score: 95.654 |
| vg0235783884 (J) | chr02 | 35783884 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os02g58540.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os02g58530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.961; most accessible tissue: Zhenshan97 panicle, score: 96.528 |
| vg0235783924 (J) | chr02 | 35783924 | A | G | 59.30% | 0.00% | G -> A |
mr1021 (All); LR P-value: 1.35E-19;
mr1029 (All); LR P-value: 2.57E-06; mr1047 (All); LR P-value: 3.79E-10; mr1189 (All); LR P-value: 1.85E-06; mr1325 (All); LR P-value: 4.36E-11; mr1326 (All); LR P-value: 2.70E-13; mr1580 (All); LR P-value: 1.13E-19; mr1625 (All); LR P-value: 5.25E-06; mr1657 (All); LR P-value: 1.01E-11; mr1744 (All); LR P-value: 1.55E-12; mr1782 (All); LR P-value: 7.88E-06; mr1796 (All); LR P-value: 1.19E-07; mr1990 (All); LR P-value: 2.92E-06; mr1064_2 (All); LR P-value: 3.51E-60; mr1270_2 (All); LR P-value: 2.00E-27; mr1316_2 (All); LR P-value: 6.52E-22; mr1323_2 (All); LR P-value: 1.72E-27; mr1326_2 (All); LR P-value: 2.04E-13; mr1744_2 (All); LR P-value: 1.44E-16; mr1745_2 (All); LR P-value: 1.01E-40; mr1782_2 (All); LR P-value: 1.55E-10; mr1932_2 (All); LR P-value: 4.57E-30; mr1970_2 (All); LR P-value: 1.37E-62; mr1973_2 (All); LR P-value: 8.78E-99 |
LOC_Os02g58540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.799; most accessible tissue: Zhenshan97 panicle, score: 96.702 |
| vg0235784118 (J) | chr02 | 35784118 | A | G | 98.80% | 0.00% | A -> G | NA |
LOC_Os02g58540.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g58530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g58550.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.171; most accessible tissue: Zhenshan97 panicle, score: 98.187 |
| vg0235784137 (J) | chr02 | 35784137 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os02g58540.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g58530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g58550.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.076; most accessible tissue: Zhenshan97 panicle, score: 98.145 |
| STR0235783761 (J) | chr02 | 35783761 | CTGC | CTGCTGC | 85.30% | 0.00% | CTGCTGC -> CTGC | NA |
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