40 variations found. Os02g0627100/LOC_Os02g41680 (phenylalanine ammonia-lyase; putative; expressed), ranging from 25,006,466 bp to 25,009,121 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g41680 | phenylalanine ammonia-lyase, putative, expressed; RAP ID: Os02g0627100; MSU ID: LOC_Os02g41680 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os02g41680 | Os02g0627100 | OsPAL1, PAL | phenylalanine ammonia-lyase 1, phenylalanine ammonia lyase | Q0DZE0. X87946. A2X7F7. | PAL1 | PHENYLALANINE AMMONIA-LYASE 1 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0225006506 (J) | chr02 | 25006506 | T | C | 97.70% | 0.00% | T -> C | NA |
LOC_Os02g41680.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 57.332; most accessible tissue: Minghui63 root, score: 90.372 |
| vg0225006575 (J) | chr02 | 25006575 | G | C | 55.00% | 0.00% | C -> G,T |
LOC_Os02g41680.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g41680.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.799; most accessible tissue: Zhenshan97 root, score: 93.268 |
|
| vg0225006672 (J) | chr02 | 25006672 | C | T | 94.20% | 0.00% | C -> T | NA |
LOC_Os02g41680.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.703; most accessible tissue: Zhenshan97 root, score: 94.941 |
| vg0225006701 (J) | chr02 | 25006701 | T | C | 94.00% | 0.00% | T -> C | NA |
LOC_Os02g41680.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.005; most accessible tissue: Zhenshan97 root, score: 95.396 |
| vg0225007028 (J) | chr02 | 25007028 | G | C | 92.60% | 0.00% | G -> C |
mr1389 (All); LR P-value: 3.87E-07;
mr1389 (Ind_All); LR P-value: 2.74E-07; mr1038_2 (All); LR P-value: 7.32E-07; mr1038_2 (Ind_All); LR P-value: 2.98E-07; mr1227_2 (All); LR P-value: 2.20E-06; mr1389_2 (All); LR P-value: 4.22E-07; mr1389_2 (Ind_All); LR P-value: 9.36E-08; mr1416_2 (Ind_All); LMM P-value: 6.91E-06; LR P-value: 6.90E-06; mr1457_2 (Ind_All); LR P-value: 3.80E-06 |
LOC_Os02g41680.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.400; most accessible tissue: Zhenshan97 root, score: 97.140 |
| vg0225007295 (J) | chr02 | 25007295 | G | T | 99.00% | 0.00% | G -> T | NA |
LOC_Os02g41680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.599; most accessible tissue: Zhenshan97 root, score: 95.791 |
| vg0225007371 (J) | chr02 | 25007371 | G | T | 62.90% | 0.00% | T -> G | NA |
LOC_Os02g41680.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 78.113; most accessible tissue: Zhenshan97 root, score: 95.366 |
| vg0225007547 (J) | chr02 | 25007547 | C | A | 97.20% | 0.00% | C -> A | NA |
LOC_Os02g41680.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.524; most accessible tissue: Zhenshan97 root, score: 94.685 |
| vg0225007569 (J) | chr02 | 25007569 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os02g41680.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 81.044; most accessible tissue: Zhenshan97 root, score: 94.705 |
| vg0225007733 (J) | chr02 | 25007733 | C | G | 75.90% | 0.00% | C -> G |
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.970; most accessible tissue: Zhenshan97 root, score: 93.988 |
|
| vg0225007748 (J) | chr02 | 25007748 | A | G | 75.90% | 0.00% | A -> G |
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.455; most accessible tissue: Zhenshan97 root, score: 94.124 |
|
| vg0225007757 (J) | chr02 | 25007757 | G | C | 76.00% | 0.00% | G -> C |
mr1593 (Ind_All); LR P-value: 1.29E-06;
mr1686 (Ind_All); LR P-value: 2.93E-06; mr1925 (All); LR P-value: 4.56E-10; mr1925 (Ind_All); LR P-value: 5.79E-07; mr1498_2 (All); LR P-value: 4.74E-07; mr1593_2 (Ind_All); LR P-value: 2.29E-08; mr1677_2 (All); LR P-value: 8.55E-06; mr1925_2 (All); LR P-value: 9.98E-07 |
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.229; most accessible tissue: Zhenshan97 root, score: 93.844 |
| vg0225007770 (J) | chr02 | 25007770 | G | A | 76.40% | 5.76% | G -> A | NA |
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.388; most accessible tissue: Zhenshan97 root, score: 94.011 |
| vg0225007771 (J) | chr02 | 25007771 | C | A | 76.40% | 5.71% | C -> A | NA |
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g41680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.224; most accessible tissue: Zhenshan97 root, score: 93.988 |
| vg0225007772 (J) | chr02 | 25007772 | G | A | 68.90% | 22.22% | G -> A |
LOC_Os02g41680.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.224; most accessible tissue: Zhenshan97 root, score: 93.988 |
|
| vg0225007778 (J) | chr02 | 25007778 | A | G | 77.10% | 21.69% | A -> G | NA |
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.846; most accessible tissue: Zhenshan97 root, score: 94.124 |
| vg0225007805 (J) | chr02 | 25007805 | T | C | 76.90% | 22.41% | T -> C |
mr1195 (All); LR P-value: 4.71E-10;
mr1593 (Ind_All); LR P-value: 1.21E-06; mr1686 (Ind_All); LR P-value: 5.22E-06; mr1925 (All); LR P-value: 1.51E-09; mr1925 (Ind_All); LR P-value: 2.03E-06; mr1498_2 (All); LR P-value: 9.44E-07; mr1593_2 (Ind_All); LR P-value: 1.51E-08; mr1925_2 (All); LR P-value: 2.20E-06 |
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 82.752; most accessible tissue: Zhenshan97 root, score: 94.168 |
| vg0225007808 (J) | chr02 | 25007808 | G | C | 76.80% | 22.37% | G -> C |
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 82.734; most accessible tissue: Zhenshan97 root, score: 94.168 |
|
| vg0225007811 (J) | chr02 | 25007811 | T | C | 76.50% | 22.60% | T -> C |
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 82.479; most accessible tissue: Zhenshan97 root, score: 94.146 |
|
| vg0225007814 (J) | chr02 | 25007814 | C | G | 76.40% | 22.18% | C -> G |
mr1195 (All); LR P-value: 4.71E-10;
mr1593 (Ind_All); LR P-value: 1.21E-06; mr1686 (Ind_All); LR P-value: 5.22E-06; mr1925 (All); LR P-value: 1.51E-09; mr1925 (Ind_All); LR P-value: 2.03E-06; mr1498_2 (All); LR P-value: 9.44E-07; mr1593_2 (Ind_All); LR P-value: 1.51E-08; mr1925_2 (All); LR P-value: 2.20E-06 |
LOC_Os02g41680.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g41680.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.500; most accessible tissue: Zhenshan97 root, score: 94.146 |
| vg0225007828 (J) | chr02 | 25007828 | G | T | 76.00% | 0.00% | G -> T |
mr1195 (All); LR P-value: 4.40E-10;
mr1593 (Ind_All); LR P-value: 5.25E-07; mr1686 (Ind_All); LR P-value: 4.70E-06; mr1925 (All); LR P-value: 2.99E-09; mr1925 (Ind_All); LR P-value: 3.84E-06; mr1195_2 (Ind_All); LR P-value: 1.60E-09; mr1498_2 (All); LR P-value: 5.25E-07; mr1593_2 (Ind_All); LR P-value: 3.73E-09; mr1925_2 (All); LR P-value: 1.45E-06 |
LOC_Os02g41680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.507; most accessible tissue: Zhenshan97 root, score: 94.343 |
| vg0225007832 (J) | chr02 | 25007832 | T | C | 76.00% | 0.00% | T -> C |
mr1195 (All); LR P-value: 4.71E-10;
mr1593 (Ind_All); LR P-value: 1.21E-06; mr1686 (Ind_All); LR P-value: 5.22E-06; mr1925 (All); LR P-value: 1.51E-09; mr1925 (Ind_All); LR P-value: 2.03E-06; mr1498_2 (All); LR P-value: 9.44E-07; mr1593_2 (Ind_All); LR P-value: 1.51E-08; mr1925_2 (All); LR P-value: 2.20E-06 |
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.503; most accessible tissue: Zhenshan97 root, score: 94.343 |
| vg0225007849 (J) | chr02 | 25007849 | G | A | 75.90% | 0.00% | G -> A |
LOC_Os02g41680.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.998; most accessible tissue: Zhenshan97 root, score: 94.102 |
|
| vg0225007850 (J) | chr02 | 25007850 | T | C | 75.90% | 0.00% | T -> C |
LOC_Os02g41680.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.988; most accessible tissue: Zhenshan97 root, score: 94.102 |
|
| vg0225007858 (J) | chr02 | 25007858 | G | T | 99.20% | 0.00% | G -> T | NA |
LOC_Os02g41680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 80.713; most accessible tissue: Zhenshan97 root, score: 94.168 |
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