17 variations found. Os08g0469100/LOC_Os08g36540 (aspartic proteinase nepenthesin-1 precursor; putative; expressed), ranging from 23,069,302 bp to 23,070,603 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os08g36540 | aspartic proteinase nepenthesin-1 precursor, putative, expressed; RAP ID: Os08g0469100; MSU ID: LOC_Os08g36540 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0823069329 (J) | chr08 | 23069329 | A | AT | 81.70% | 7.26% | A -> AT | NA |
LOC_Os08g36540.1 Alt: AT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.674; most accessible tissue: Minghui63 root, score: 93.106 |
| vg0823069333 (J) | chr08 | 23069333 | TGC | TTGTGAA AACACTT GAGAACC AAGCATC ACTAGC | 79.40% | 7.62% | TGC -> TTGTGAAAAC ACTTGAGAAC CAAGCATCAC TAGC,T,TTG TGAAAACACT TGAGAACCAA GC,TTGTGAA AACACTTGAG C,TTGTGAAA ACACTTGAGA ACCAAGCATC ACTAGCTACT GCCCATGTCC TGATTCATTG TACTAGC,TT GTGAAAACAC TTGAGAACCA AGCATCACTA GCTACTGCCC GTGTCCTGAT TCATTGTACT AGC | NA |
LOC_Os08g36540.1 Alt: TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os08g36540.1 Alt: TTGTGAAAACACTTGAGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os08g36540.1 Alt: TTGTGAAAACACTTGAGAACCAAGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: TTGTGAAAACACTTGAGAACCAAGCATCACTAGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTCCTGATTCATTGTACTAGC| frameshift_variant HIGH(snpEff) LOC_Os08g36530.1 Alt: TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTCCTGATTCATTGTACTAGC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTCCTGATTCATTGTACTAGC| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.928; most accessible tissue: Minghui63 root, score: 93.342 |
| vg0823069334 (J) | chr08 | 23069334 | G | GTGAAAA CA | 83.00% | 7.79% | G -> GTGAAAACAC TTGAGAACCA AGCATCACTA GCTACTGCCC ATGTC,GTGA AAACACTTGA GAACCAAGCA TCA,GTGAAA ACA,GTGAAA ACACTTGAGA ACCAAGCATC ACTAGCTACT GCCCATGTCC TGATTCATTG TA,GTGAAAA CACTTGAGAA CCAAGCATCA CTAGCTA,GT GAAAACACTT GAGAACCAAG CATCACTAGC TACTGCCCGT GTC | NA |
LOC_Os08g36540.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTA| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar)
LOC_Os08g36540.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTC| frameshift_variant&stop_gained HIGH(snpEff) LOC_Os08g36530.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: GTGAAAACACTTGAGAACCAAGCATCA| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTC| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTA| stop_gained&inframe_insertion HIGH(snpEff) LOC_Os08g36530.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTA| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: GTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTA| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: GTGAAAACA| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 81.577; most accessible tissue: Minghui63 root, score: 93.031 |
| vg0823069335 (J) | chr08 | 23069335 | C | CA | 83.20% | 7.83% | C -> CATCACTAGC TACTGCCCAT GTCCTGA,CA ,G,CATCACT AGCTACTGCC CATGTCCTGA TTCATTGTAC TAGA | NA |
LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os08g36540.1 Alt: CA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: G| missense_variant MODERATE(snpEff) LOC_Os08g36530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: CATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGA| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os08g36540.1 Alt: CATCACTAGCTACTGCCCATGTCCTGA| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 81.577; most accessible tissue: Minghui63 root, score: 93.031 |
| vg0823069336 (J) | chr08 | 23069336 | T | TACTGCC | 99.70% | 0.00% | T -> TGTGAAAA,T ACTGCC,TTG AGAAC | NA |
LOC_Os08g36540.1 Alt: TTGAGAAC| frameshift_variant HIGH(snpEff)
LOC_Os08g36530.1 Alt: TTGAGAAC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: TTGAGAAC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: TACTGCC| disruptive_inframe_insertion MODERATE(snpEff) LOC_Os08g36530.1 Alt: TACTGCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: TACTGCC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: TGTGAAAA| frameshift_variant&stop_gained HIGH(snpEff) LOC_Os08g36530.1 Alt: TGTGAAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: TGTGAAAA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.681; most accessible tissue: Minghui63 root, score: 93.056 |
| vg0823069337 (J) | chr08 | 23069337 | C | CACTAGC TACTGCC CATGTCC TG | 99.80% | 0.00% | C -> CACTAGCTAC TGCCCATGTC CTG,G,CACT AGCTACTGCC CGTGTCCTG | NA |
LOC_Os08g36540.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os08g36530.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: CACTAGCTACTGCCCGTGTCCTG| frameshift_variant HIGH(snpEff) LOC_Os08g36530.1 Alt: CACTAGCTACTGCCCGTGTCCTG| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: CACTAGCTACTGCCCGTGTCCTG| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: CACTAGCTACTGCCCATGTCCTG| frameshift_variant HIGH(snpEff) LOC_Os08g36530.1 Alt: CACTAGCTACTGCCCATGTCCTG| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: CACTAGCTACTGCCCATGTCCTG| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.716; most accessible tissue: Minghui63 root, score: 93.081 |
| vg0823069371 (J) | chr08 | 23069371 | GGCACGC CAC | G | 66.60% | 0.19% | G -> GGCACGCCAC | NA |
LOC_Os08g36540.1 Alt: GGCACGCCAC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.167; most accessible tissue: Minghui63 root, score: 92.801 |
| vg0823069372 (J) | chr08 | 23069372 | C | T | 66.60% | 0.19% | T -> C | NA |
LOC_Os08g36540.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.167; most accessible tissue: Minghui63 root, score: 92.801 |
| vg0823069450 (J) | chr08 | 23069450 | TGGCGGC GAGGCAC GGCT | CGGCGGC GAGGCAC GGCT | 66.50% | 0.00% | CGGCGGCGAG GCACGGCT -> TGGCGGCGAG GCACGGCT,C | NA |
LOC_Os08g36540.1 Alt: TGGCGGCGAGGCACGGCT| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g36540.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 84.567; most accessible tissue: Minghui63 root, score: 90.642 |
| vg0823069469 (J) | chr08 | 23069469 | G | C | 99.20% | 0.00% | G -> C | NA |
LOC_Os08g36540.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os08g36530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.026; most accessible tissue: Minghui63 root, score: 89.635 |
| vg0823069523 (J) | chr08 | 23069523 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os08g36540.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os08g36530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.944; most accessible tissue: Minghui63 flag leaf, score: 88.459 |
| vg0823069611 (J) | chr08 | 23069611 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os08g36540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 78.766; most accessible tissue: Zhenshan97 flag leaf, score: 88.363 |
| vg0823069612 (J) | chr08 | 23069612 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os08g36540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 78.488; most accessible tissue: Zhenshan97 flag leaf, score: 88.363 |
| vg0823069856 (J) | chr08 | 23069856 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os08g36540.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os08g36530.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g36550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.073; most accessible tissue: Zhenshan97 young leaf, score: 86.383 |
| vg0823069917 (J) | chr08 | 23069917 | A | G | 66.40% | 0.40% | G -> A |
mr1005 (All); LR P-value: 1.16E-08;
mr1071 (All); LR P-value: 4.48E-89; mr1080 (All); LR P-value: 1.47E-80; mr1100 (All); LR P-value: 1.08E-76; mr1136 (All); LR P-value: 5.85E-45; mr1140 (All); LR P-value: 1.89E-91; mr1141 (All); LR P-value: 1.83E-43; mr1191 (All); LR P-value: 1.93E-09; mr1203 (All); LR P-value: 2.63E-97; mr1238 (All); LR P-value: 1.13E-26; mr1243 (All); LR P-value: 9.52E-33; mr1309 (All); LR P-value: 7.19E-28; mr1395 (All); LR P-value: 4.70E-91; mr1448 (All); LR P-value: 4.90E-32; mr1480 (All); LR P-value: 1.32E-41; mr1484 (All); LR P-value: 1.16E-15; mr1566 (All); LR P-value: 1.07E-17; mr1591 (All); LR P-value: 3.76E-44; mr1594 (All); LR P-value: 5.53E-57; mr1599 (All); LR P-value: 1.27E-49; mr1613 (All); LR P-value: 2.54E-76; mr1618 (All); LR P-value: 5.51E-92; mr1619 (All); LR P-value: 1.38E-65; mr1629 (All); LR P-value: 2.58E-77; mr1689 (All); LR P-value: 6.74E-21; mr1692 (All); LR P-value: 1.77E-48; mr1758 (All); LR P-value: 9.45E-86; mr1828 (All); LR P-value: 1.87E-36; mr1841 (All); LR P-value: 4.09E-23; mr1890 (All); LR P-value: 7.85E-41; mr1891 (All); LR P-value: 7.05E-41; mr1900 (All); LR P-value: 3.55E-13; mr1905 (All); LR P-value: 1.57E-10; mr1915 (All); LR P-value: 6.42E-07; mr1968 (All); LR P-value: 3.17E-17; mr1141_2 (All); LR P-value: 1.23E-53; mr1194_2 (All); LR P-value: 3.73E-53; mr1203_2 (All); LR P-value: 3.36E-111; mr1276_2 (All); LR P-value: 4.33E-19; mr1448_2 (All); LR P-value: 1.21E-34; mr1480_2 (All); LR P-value: 1.20E-54; mr1484_2 (All); LR P-value: 1.94E-25; mr1617_2 (All); LR P-value: 6.09E-26; mr1619_2 (All); LR P-value: 1.35E-98; mr1695_2 (All); LR P-value: 1.26E-59; mr1711_2 (All); LR P-value: 1.68E-85; mr1828_2 (All); LR P-value: 5.56E-69; mr1841_2 (All); LR P-value: 1.62E-31; mr1900_2 (All); LR P-value: 2.17E-19; mr1944_2 (All); LR P-value: 3.27E-41; mr1945_2 (All); LR P-value: 1.01E-18; mr1968_2 (All); LR P-value: 1.16E-23 |
LOC_Os08g36540.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g36540.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.961; most accessible tissue: Zhenshan97 young leaf, score: 88.127 |
| vg0823069973 (J) | chr08 | 23069973 | C | T | 87.80% | 0.00% | C -> T | NA |
LOC_Os08g36540.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.718; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0823070595 (J) | chr08 | 23070595 | A | T | 66.60% | 0.32% | T -> A | NA |
LOC_Os08g36540.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g36530.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g36550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.370; most accessible tissue: Minghui63 root, score: 72.134 |