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Search Results:

9 variations found. Os11g0138700/LOC_Os11g04330 (OsFBK24 - F-box domain and kelch repeat containing protein; expressed), ranging from 1,801,183 bp to 1,802,662 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os11g04330 OsFBK24 - F-box domain and kelch repeat containing protein, expressed; RAP ID: Os11g0138700; MSU ID: LOC_Os11g04330

Gene Expression Atlas:

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.

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

ColorExplainDetails
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.

Detailed Variation Information:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg1101801245 (J) chr11 1801245 C G 79.20% 0.00% C -> G
Heading_date (Ind_All); LR P-value: 2.90E-10;
mr1170 (Ind_All); LR P-value: 8.98E-06;
mr1598 (Ind_All); LR P-value: 1.46E-06;
mr1835 (All); LR P-value: 1.48E-06;
mr1904 (All); LR P-value: 9.16E-14;
mr1904 (Ind_All); LMM P-value: 8.94E-06; LR P-value: 1.88E-11;
mr1024_2 (Ind_All); LR P-value: 5.01E-07;
mr1072_2 (Ind_All); LR P-value: 1.93E-07;
mr1075_2 (Ind_All); LR P-value: 1.31E-07;
mr1077_2 (Ind_All); LR P-value: 2.96E-08;
mr1265_2 (All); LR P-value: 1.69E-06;
mr1528_2 (All); LR P-value: 2.32E-07;
mr1531_2 (Ind_All); LR P-value: 1.02E-06;
mr1558_2 (Ind_All); LR P-value: 9.53E-07;
mr1565_2 (Ind_All); LR P-value: 6.04E-12;
mr1598_2 (Ind_All); LR P-value: 4.83E-10;
mr1659_2 (Ind_All); LR P-value: 1.04E-06;
mr1835_2 (Ind_All); LR P-value: 5.27E-06;
mr1861_2 (Ind_All); LR P-value: 2.24E-10;
mr1904_2 (Ind_All); LR P-value: 6.58E-08;
mr1962_2 (Ind_All); LR P-value: 9.57E-09
LOC_Os11g04330.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04320.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04340.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.933; most accessible tissue: Zhenshan97 panicle, score: 96.414
vg1101801324 (J) chr11 1801324 A C 98.80% 0.11% A -> C NA
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g04330.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.143; most accessible tissue: Zhenshan97 panicle, score: 96.335
vg1101801390 (J) chr11 1801390 T C 65.60% 0.00% C -> T NA
LOC_Os11g04330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 82.938; most accessible tissue: Zhenshan97 panicle, score: 95.438
vg1101801520 (J) chr11 1801520 C T 99.20% 0.00% C -> T NA
LOC_Os11g04330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.133; most accessible tissue: Zhenshan97 panicle, score: 94.740
vg1101801545 (J) chr11 1801545 G T 99.30% 0.00% G -> T NA
LOC_Os11g04330.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g04310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g04320.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g04340.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 85.547; most accessible tissue: Zhenshan97 panicle, score: 94.668
vg1101801666 (J) chr11 1801666 C T 79.10% 0.00% C -> T
Heading_date (Ind_All); LR P-value: 2.90E-10;
mr1170 (Ind_All); LR P-value: 8.98E-06;
mr1598 (Ind_All); LR P-value: 1.46E-06;
mr1681 (All); LR P-value: 3.17E-06;
mr1835 (All); LR P-value: 1.73E-06;
mr1904 (All); LR P-value: 1.11E-13;
mr1904 (Ind_All); LMM P-value: 8.94E-06; LR P-value: 1.88E-11;
mr1024_2 (Ind_All); LR P-value: 5.01E-07;
mr1072_2 (Ind_All); LR P-value: 1.93E-07;
mr1075_2 (Ind_All); LR P-value: 1.31E-07;
mr1077_2 (Ind_All); LR P-value: 2.96E-08;
mr1265_2 (All); LR P-value: 1.93E-06;
mr1528_2 (All); LR P-value: 7.07E-08;
mr1531_2 (Ind_All); LR P-value: 1.02E-06;
mr1558_2 (Ind_All); LR P-value: 9.53E-07;
mr1565_2 (Ind_All); LR P-value: 6.04E-12;
mr1598_2 (Ind_All); LR P-value: 4.83E-10;
mr1659_2 (Ind_All); LR P-value: 1.04E-06;
mr1835_2 (Ind_All); LR P-value: 5.27E-06;
mr1861_2 (Ind_All); LR P-value: 2.24E-10;
mr1904_2 (Ind_All); LR P-value: 6.58E-08;
mr1962_2 (Ind_All); LR P-value: 9.57E-09
LOC_Os11g04330.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 84.653; most accessible tissue: Zhenshan97 panicle, score: 94.195
vg1101802168 (J) chr11 1802168 C G 95.50% 1.12% C -> G NA
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g04330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.898; most accessible tissue: Zhenshan97 root, score: 95.274
vg1101802207 (J) chr11 1802207 C T 96.00% 1.12% C -> T NA
LOC_Os11g04330.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.221; most accessible tissue: Zhenshan97 root, score: 95.258
vg1101802247 (J) chr11 1802247 T G 95.90% 1.12% T -> G NA
LOC_Os11g04330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g04330.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.015; most accessible tissue: Zhenshan97 root, score: 95.226