27 variations found. Os06g0222400/LOC_Os06g11860 (ethylene-responsive transcription factor; putative; expressed), ranging from 6,304,587 bp to 6,306,661 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os06g11860 | ethylene-responsive transcription factor, putative, expressed; RAP ID: Os06g0222400; MSU ID: LOC_Os06g11860 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os06g11860 | Os06g0222400 | OsERF#120, OsERF120, AP2/EREBP#105, AP2/EREBP105 | ethylene response factor 120, APETALA2/ethylene-responsive element binding protein 105 | ERF120 | ETHYLENE RESPONSE FACTOR 120 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0606304728 (J) | chr06 | 6304728 | ACTACT | ACTACG | 70.40% | 0.00% | ACTACT -> ACTACG | NA |
|
| vg0606304686 (J) | chr06 | 6304686 | A | T | 63.40% | 0.00% | T -> A |
mr1798 (Jap_All); LR P-value: 2.78E-06;
mr1077_2 (Jap_All); LR P-value: 2.13E-06; mr1336_2 (Ind_All); LR P-value: 3.36E-07; mr1579_2 (Ind_All); LR P-value: 2.53E-07; mr1798_2 (Jap_All); LR P-value: 9.09E-08; mr1870_2 (Jap_All); LR P-value: 2.95E-06; mr1877_2 (Jap_All); LMM P-value: 8.45E-06; LR P-value: 8.45E-06 |
LOC_Os06g11860.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 78.669; most accessible tissue: Callus, score: 95.402 |
| vg0606304687 (J) | chr06 | 6304687 | GA | GAA | 97.80% | 0.00% | GA -> GAA,G,GAAA | NA |
LOC_Os06g11860.1 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g11860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g11860.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.669; most accessible tissue: Callus, score: 95.402 |
| vg0606304733 (J) | chr06 | 6304733 | T | G | 86.50% | 0.00% | T -> G | NA |
LOC_Os06g11860.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 78.747; most accessible tissue: Callus, score: 95.402 |
| vg0606304811 (J) | chr06 | 6304811 | CGAT | C | 86.50% | 0.00% | CGAT -> C | NA |
LOC_Os06g11860.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.058; most accessible tissue: Zhenshan97 panicle, score: 95.855 |
| vg0606304814 (J) | chr06 | 6304814 | T | C | 50.10% | 0.00% | T -> C |
mr1798 (Jap_All); LR P-value: 2.78E-06;
mr1077_2 (Jap_All); LR P-value: 2.13E-06; mr1336_2 (Ind_All); LR P-value: 4.79E-08; mr1579_2 (Ind_All); LMM P-value: 8.28E-06; LR P-value: 1.35E-08; mr1798_2 (Jap_All); LR P-value: 9.09E-08; mr1870_2 (Jap_All); LR P-value: 2.95E-06; mr1877_2 (Jap_All); LMM P-value: 8.45E-06; LR P-value: 8.45E-06 |
LOC_Os06g11860.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.381; most accessible tissue: Zhenshan97 panicle, score: 95.903 |
| vg0606304829 (J) | chr06 | 6304829 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os06g11860.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.483; most accessible tissue: Zhenshan97 panicle, score: 95.997 |
| vg0606304923 (J) | chr06 | 6304923 | T | C | 98.40% | 0.00% | T -> C | NA |
LOC_Os06g11860.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.293; most accessible tissue: Zhenshan97 panicle, score: 96.173 |
| vg0606304949 (J) | chr06 | 6304949 | GA | G | 99.70% | 0.00% | GA -> G | NA |
LOC_Os06g11860.1 Alt: G| frameshift_variant HIGH(snpEff)
LOC_Os06g11870.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.019; most accessible tissue: Zhenshan97 panicle, score: 96.335 |
| vg0606305064 (J) | chr06 | 6305064 | G | C | 60.00% | 0.34% | C -> G | NA |
LOC_Os06g11860.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g11860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.234; most accessible tissue: Zhenshan97 panicle, score: 96.863 |
| vg0606305101 (J) | chr06 | 6305101 | G | A | 62.40% | 0.38% | A -> G | NA |
LOC_Os06g11860.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g11860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.533; most accessible tissue: Zhenshan97 panicle, score: 96.599 |
| vg0606305147 (J) | chr06 | 6305147 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os06g11860.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.805; most accessible tissue: Zhenshan97 panicle, score: 96.801 |
| vg0606305179 (J) | chr06 | 6305179 | A | AGCG | 72.40% | 0.00% | A -> AGCG,AGCGG CGGCG | NA |
LOC_Os06g11860.1 Alt: AGCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g11860.1 Alt: AGCGGCGGCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 85.210; most accessible tissue: Zhenshan97 panicle, score: 96.254 |
| vg0606305386 (J) | chr06 | 6305386 | G | T | 78.80% | 8.00% | G -> T | NA |
LOC_Os06g11860.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g11860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.813; most accessible tissue: Zhenshan97 panicle, score: 94.518 |
| vg0606305494 (J) | chr06 | 6305494 | GGCCGCC | GGCCGCC GCC | 55.10% | 5.61% | GGCCGCCGCC -> GGCCGCC,G | NA |
LOC_Os06g11860.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g11860.1 Alt: GGCCGCC| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os06g11860.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.542; most accessible tissue: Zhenshan97 panicle, score: 94.112 |
| vg0606305654 (J) | chr06 | 6305654 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os06g11860.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os06g11870.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.008; most accessible tissue: Zhenshan97 panicle, score: 91.206 |
| vg0606305896 (J) | chr06 | 6305896 | C | CGTGGAG GTGGAG | 82.90% | 0.00% | C -> CGTGGAGGTG GAG,CGTGGA G | NA |
LOC_Os06g11860.1 Alt: CGTGGAGGTGGAG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g11860.1 Alt: CGTGGAG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 75.150; most accessible tissue: Zhenshan97 young leaf, score: 89.450 |
| vg0606305907 (J) | chr06 | 6305907 | A | AGGTGGA GGTGTT | 54.60% | 0.00% | A -> AGGTGGAGGT GTT | NA |
LOC_Os06g11860.1 Alt: AGGTGGAGGTGTT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 75.071; most accessible tissue: Zhenshan97 young leaf, score: 89.559 |
| vg0606306190 (J) | chr06 | 6306190 | T | G | 63.40% | 0.00% | G -> T |
mr1798 (Jap_All); LR P-value: 2.78E-06;
mr1077_2 (Jap_All); LR P-value: 2.13E-06; mr1336_2 (Ind_All); LR P-value: 1.13E-07; mr1579_2 (Ind_All); LR P-value: 4.58E-08; mr1798_2 (Jap_All); LR P-value: 9.09E-08; mr1870_2 (Jap_All); LR P-value: 2.95E-06; mr1877_2 (Jap_All); LMM P-value: 8.45E-06; LR P-value: 8.45E-06 |
LOC_Os06g11860.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g11870.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.701; most accessible tissue: Zhenshan97 flower, score: 94.277 |
| vg0606306214 (J) | chr06 | 6306214 | TA | T | 87.60% | 0.00% | TA -> T,TAA | NA |
LOC_Os06g11860.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g11870.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g11860.1 Alt: TAA| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os06g11870.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.726; most accessible tissue: Zhenshan97 flower, score: 95.157 |
| vg0606306222 (J) | chr06 | 6306222 | AAAG | A | 97.50% | 0.00% | AAAG -> A | NA |
LOC_Os06g11860.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g11870.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.559; most accessible tissue: Zhenshan97 flower, score: 95.196 |
| vg0606306224 (J) | chr06 | 6306224 | A | G | 99.30% | 0.00% | A -> G | NA |
LOC_Os06g11860.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g11870.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.561; most accessible tissue: Zhenshan97 flower, score: 95.222 |
| vg0606306268 (J) | chr06 | 6306268 | G | A | 97.50% | 0.00% | G -> A | NA |
LOC_Os06g11860.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g11870.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.685; most accessible tissue: Zhenshan97 flower, score: 95.349 |
| vg0606306454 (J) | chr06 | 6306454 | CT | C | 99.60% | 0.00% | CT -> C | NA |
LOC_Os06g11860.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os06g11870.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.794; most accessible tissue: Zhenshan97 flower, score: 98.120 |
| vg0606306591 (J) | chr06 | 6306591 | A | G | 99.50% | 0.00% | A -> G | NA |
LOC_Os06g11860.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os06g11870.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.640; most accessible tissue: Minghui63 root, score: 99.627 |
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