16 variations found. Os03g0777000/LOC_Os03g56580 (no apical meristem protein; putative; expressed), ranging from 32,234,310 bp to 32,236,602 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g56580 | no apical meristem protein, putative, expressed; RAP ID: Os03g0777000; MSU ID: LOC_Os03g56580 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os03g56580 | Os03g0777000 | ONAC066, ONAC66 | NAC domain-containing protein 066, NAC domain-containing protein 66 | NAC66 | NAC DOMAIN-CONTAINING PROTEIN 66 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0332234425 (J) | chr03 | 32234425 | A | G | 64.70% | 0.11% | G -> A | NA |
LOC_Os03g56580.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56572.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.722; most accessible tissue: Zhenshan97 root, score: 90.785 |
| vg0332234437 (J) | chr03 | 32234437 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os03g56580.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g56572.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g56590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.562; most accessible tissue: Zhenshan97 root, score: 90.684 |
| vg0332235209 (J) | chr03 | 32235209 | T | A | 64.70% | 0.13% | A -> T | NA |
LOC_Os03g56590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.826; most accessible tissue: Zhenshan97 root, score: 92.108 |
| vg0332235251 (J) | chr03 | 32235251 | GACA | G | 64.60% | 0.44% | G -> GACA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g56590.1 Alt: GACA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56580.1 Alt: GACA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.632; most accessible tissue: Callus, score: 91.876 |
| vg0332235283 (J) | chr03 | 32235283 | A | G | 64.60% | 0.28% | G -> A | NA |
LOC_Os03g56590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56580.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.965; most accessible tissue: Zhenshan97 root, score: 92.323 |
| vg0332235417 (J) | chr03 | 32235417 | T | C | 64.60% | 0.21% | C -> T | NA |
LOC_Os03g56590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56580.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.830; most accessible tissue: Zhenshan97 root, score: 92.253 |
| vg0332235442 (J) | chr03 | 32235442 | AT | A | 64.60% | 0.28% | A -> AT,ATT | NA |
LOC_Os03g56590.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56580.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g56590.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56580.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.511; most accessible tissue: Callus, score: 92.509 |
| vg0332235545 (J) | chr03 | 32235545 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os03g56590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g56580.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.490; most accessible tissue: Zhenshan97 root, score: 92.529 |
| vg0332235783 (J) | chr03 | 32235783 | CCGCCGG CGCCGG | C | 62.70% | 0.00% | C -> CCGCCGGCGC CGG,CCGCCG G | NA |
LOC_Os03g56580.1 Alt: CCGCCGGCGCCGG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os03g56580.1 Alt: CCGCCGG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 90.623; most accessible tissue: Zhenshan97 flag leaf, score: 95.995 |
| vg0332235792 (J) | chr03 | 32235792 | A | C | 99.50% | 0.00% | A -> C | NA |
LOC_Os03g56580.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g56590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.781; most accessible tissue: Zhenshan97 flag leaf, score: 95.984 |
| vg0332235796 (J) | chr03 | 32235796 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os03g56580.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g56590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.704; most accessible tissue: Zhenshan97 flag leaf, score: 96.007 |
| vg0332235797 (J) | chr03 | 32235797 | GA | G | 99.80% | 0.00% | GA -> G | NA |
LOC_Os03g56580.1 Alt: G| frameshift_variant HIGH(snpEff)
The average chromatin accessibility score: 90.604; most accessible tissue: Zhenshan97 flag leaf, score: 95.973 |
| vg0332236139 (J) | chr03 | 32236139 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os03g56580.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g56590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.621; most accessible tissue: Zhenshan97 flag leaf, score: 97.402 |
| vg0332236259 (J) | chr03 | 32236259 | GAA | G | 64.70% | 0.06% | G -> GAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g56580.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g56590.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.605; most accessible tissue: Minghui63 flag leaf, score: 98.252 |
| vg0332236300 (J) | chr03 | 32236300 | G | A | 88.70% | 0.00% | G -> A |
mr1028 (All); LR P-value: 1.73E-06;
mr1126 (All); LR P-value: 4.90E-07; mr1146 (All); LR P-value: 2.11E-14; mr1244 (All); LR P-value: 1.07E-20; mr1652 (All); LR P-value: 2.26E-06; mr1730 (All); LR P-value: 1.12E-10; mr1918 (All); LR P-value: 5.98E-14; mr1929 (All); LR P-value: 2.10E-08; mr1931 (All); LR P-value: 1.41E-06; mr1138_2 (Ind_All); LR P-value: 1.12E-06; mr1587_2 (All); LR P-value: 1.48E-15 |
LOC_Os03g56580.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g56590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.304; most accessible tissue: Zhenshan97 root, score: 98.180 |
| STR0332235443 (J) | chr03 | 32235443 | TT | T | 63.30% | 0.00% | T -> TT | NA |
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