21 variations found. Os03g0624600/LOC_Os03g42630 (No apical meristem protein; putative; expressed), ranging from 23,734,579 bp to 23,736,564 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g42630 | No apical meristem protein, putative, expressed; RAP ID: Os03g0624600; MSU ID: LOC_Os03g42630 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os03g42630 | Os03g0624600 | ONAC006, ONAC6 | NAC domain-containing protein 006, NAC domain-containing protein 6 | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0323734673 (J) | chr03 | 23734673 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os03g42630.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42650.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.228; most accessible tissue: Zhenshan97 root, score: 96.510 |
| vg0323734872 (J) | chr03 | 23734872 | CAGTAAG TGTGTTT AGCTTTA AAAACG | C | 67.20% | 0.00% | CAGTAAGTGT GTTTAGCTTT AAAAACG -> C | NA |
LOC_Os03g42650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.607; most accessible tissue: Zhenshan97 root, score: 90.081 |
| vg0323734923 (J) | chr03 | 23734923 | CATATTG AGGATT | C | 73.20% | 0.47% | CATATTGAGG ATT -> C | NA |
LOC_Os03g42650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.149; most accessible tissue: Zhenshan97 root, score: 89.064 |
| vg0323735156 (J) | chr03 | 23735156 | G | A | 95.20% | 0.00% | G -> A |
LOC_Os03g42650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.482; most accessible tissue: Minghui63 root, score: 82.967 |
|
| vg0323735221 (J) | chr03 | 23735221 | T | G | 99.50% | 0.00% | T -> G | NA |
LOC_Os03g42650.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.662; most accessible tissue: Minghui63 root, score: 82.667 |
| vg0323735248 (J) | chr03 | 23735248 | G | A | 78.00% | 0.44% | G -> A | NA |
LOC_Os03g42650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.547; most accessible tissue: Callus, score: 82.548 |
| vg0323735325 (J) | chr03 | 23735325 | T | C | 59.00% | 0.00% | C -> T |
Spikelet_length (Ind_All); LR P-value: 2.11E-07;
mr1236 (Ind_All); LR P-value: 9.74E-06; mr1408 (All); LR P-value: 1.95E-06; mr1553 (All); LR P-value: 6.84E-12; mr1663 (All); LR P-value: 1.98E-09; mr1740 (All); LR P-value: 3.54E-13; mr1785 (All); LR P-value: 4.21E-07; mr1915 (All); LR P-value: 6.14E-07; mr1553_2 (All); LR P-value: 7.37E-15 |
LOC_Os03g42650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.610; most accessible tissue: Minghui63 flower, score: 83.493 |
| vg0323735375 (J) | chr03 | 23735375 | C | CAT | 43.10% | 16.74% | CAT -> C | NA |
LOC_Os03g42650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 74.264; most accessible tissue: Minghui63 flower, score: 85.000 |
| vg0323735377 (J) | chr03 | 23735377 | TATCACT GCATGCA TA | T | 78.30% | 0.00% | TATCACTGCA TGCATA -> T | NA |
LOC_Os03g42650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.252; most accessible tissue: Minghui63 flower, score: 84.900 |
| vg0323735900 (J) | chr03 | 23735900 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os03g42630.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.455; most accessible tissue: Zhenshan97 young leaf, score: 91.689 |
| vg0323735909 (J) | chr03 | 23735909 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os03g42630.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.081; most accessible tissue: Zhenshan97 young leaf, score: 90.638 |
| vg0323735929 (J) | chr03 | 23735929 | G | C | 61.70% | 0.00% | G -> C | NA |
LOC_Os03g42630.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.067; most accessible tissue: Zhenshan97 young leaf, score: 90.363 |
| vg0323735963 (J) | chr03 | 23735963 | C | T | 64.80% | 0.00% | T -> C | NA |
LOC_Os03g42630.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.448; most accessible tissue: Zhenshan97 young leaf, score: 90.456 |
| vg0323735982 (J) | chr03 | 23735982 | G | C | 64.70% | 0.00% | C -> G | NA |
LOC_Os03g42630.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.374; most accessible tissue: Zhenshan97 young leaf, score: 90.728 |
| vg0323736025 (J) | chr03 | 23736025 | C | G | 66.30% | 0.00% | C -> G | NA |
LOC_Os03g42630.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.372; most accessible tissue: Zhenshan97 young leaf, score: 90.728 |
| vg0323736149 (J) | chr03 | 23736149 | G | A | 66.30% | 0.00% | A -> G | NA |
LOC_Os03g42630.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.810; most accessible tissue: Zhenshan97 young leaf, score: 90.638 |
| vg0323736182 (J) | chr03 | 23736182 | A | T | 79.50% | 0.00% | A -> T | NA |
LOC_Os03g42630.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.492; most accessible tissue: Zhenshan97 young leaf, score: 89.666 |
| vg0323736183 (J) | chr03 | 23736183 | G | C | 99.80% | 0.00% | G -> C | NA |
LOC_Os03g42630.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g42650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42650.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.822; most accessible tissue: Zhenshan97 young leaf, score: 90.078 |
| vg0323736191 (J) | chr03 | 23736191 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os03g42630.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g42650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g42650.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.643; most accessible tissue: Zhenshan97 young leaf, score: 89.978 |
| vg0323736433 (J) | chr03 | 23736433 | T | TATTA | 64.20% | 0.00% | TATTA -> T | NA |
LOC_Os03g42630.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g42650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g42650.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.139; most accessible tissue: Zhenshan97 root, score: 87.908 |
| STR0323736434 (J) | chr03 | 23736434 | ATTAATT AAT | ATTAATT AATTAAT | 65.00% | 0.00% | ATTAATTAAT TAAT -> ATTAATTAAT | NA |
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