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Search Results:

25 variations found. Os11g0214900/LOC_Os11g10850 (dirigent; putative; expressed), ranging from 5,978,416 bp to 5,978,986 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os11g10850 dirigent, putative; RAP ID: Os11g0214900; MSU ID: LOC_Os11g10850

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
vg1105978416 (J) chr11 5978416 A T 48.70% 47.61% A -> T
mr1216 (Ind_All); LR P-value: 4.62E-06;
mr1521 (All); LR P-value: 1.82E-12;
mr1740 (Jap_All); LR P-value: 4.33E-06;
mr1835 (All); LR P-value: 4.87E-07;
mr1648_2 (All); LR P-value: 6.27E-06
LOC_Os11g10850.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10860.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10840.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10840-LOC_Os11g10850 Alt: T| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 87.302; most accessible tissue: Zhenshan97 flag leaf, score: 95.292
vg1105978435 (J) chr11 5978435 G A 48.70% 47.14% G -> A
mr1216 (Ind_All); LR P-value: 1.52E-06;
mr1521 (All); LR P-value: 1.78E-12;
mr1740 (Jap_All); LR P-value: 6.58E-06;
mr1835 (All); LR P-value: 7.81E-07
LOC_Os11g10850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.628; most accessible tissue: Zhenshan97 flag leaf, score: 95.818
vg1105978441 (J) chr11 5978441 G A 33.40% 44.24% G -> A,C NA
LOC_Os11g10850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.671; most accessible tissue: Zhenshan97 flag leaf, score: 95.854
vg1105978492 (J) chr11 5978492 TCCACCA CCACCA TCCACCA CCA 50.90% 0.00% TCCACCACCA -> TCCACCACCA CCA,T,TCCA ,TCCACCACC ACCACCA NA
LOC_Os11g10850.1 Alt: TCCACCACCACCA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g10850.1 Alt: T| inframe_deletion MODERATE(snpEff)
LOC_Os11g10860.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g10840.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g10850.1 Alt: TCCACCACCACCACCA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g10850.1 Alt: TCCA| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 89.081; most accessible tissue: Zhenshan97 flag leaf, score: 95.866
vg1105978496 (J) chr11 5978496 C T 99.60% 0.00% C -> T NA
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 89.247; most accessible tissue: Zhenshan97 flag leaf, score: 95.902
vg1105978502 (J) chr11 5978502 C T 99.60% 0.00% C -> T NA
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 89.464; most accessible tissue: Zhenshan97 flag leaf, score: 95.925
vg1105978552 (J) chr11 5978552 T G 52.20% 0.00% G -> T
mr1216 (Ind_All); LR P-value: 6.56E-06;
mr1521 (All); LR P-value: 7.99E-13;
mr1740 (Jap_All); LR P-value: 4.33E-06;
mr1835 (All); LR P-value: 9.65E-07;
mr1648_2 (All); LR P-value: 7.95E-06
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.656; most accessible tissue: Zhenshan97 flag leaf, score: 96.683
vg1105978587 (J) chr11 5978587 C CTTG 49.10% 8.68% C -> CTTG NA
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10850.1 Alt: CTTG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 86.656; most accessible tissue: Zhenshan97 flag leaf, score: 96.856
vg1105978588 (J) chr11 5978588 C T 49.00% 5.61% C -> T NA
LOC_Os11g10850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.696; most accessible tissue: Zhenshan97 flag leaf, score: 96.894
vg1105978591 (J) chr11 5978591 C T 48.90% 50.55% C -> T NA
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.034; most accessible tissue: Zhenshan97 flag leaf, score: 97.078
vg1105978596 (J) chr11 5978596 C T 50.70% 3.20% C -> T NA
LOC_Os11g10850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 87.140; most accessible tissue: Zhenshan97 flag leaf, score: 97.098
vg1105978598 (J) chr11 5978598 GCGACAA CGGCAAC GGCAACG GCAA G 48.90% 9.35% GCGACAACGG CAACGGCAAC GGCAA -> G NA
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10850.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 87.171; most accessible tissue: Zhenshan97 flag leaf, score: 97.105
vg1105978601 (J) chr11 5978601 A G 76.00% 17.90% A -> G NA
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10850.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.180; most accessible tissue: Zhenshan97 flag leaf, score: 97.112
vg1105978628 (J) chr11 5978628 G A 52.50% 0.11% A -> G NA
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10850.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.665; most accessible tissue: Zhenshan97 flag leaf, score: 96.336
vg1105978647 (J) chr11 5978647 T G 52.30% 0.00% G -> T
mr1216 (Ind_All); LR P-value: 5.06E-07;
mr1521 (All); LR P-value: 5.99E-13;
mr1740 (Jap_All); LR P-value: 3.68E-06;
mr1835 (All); LR P-value: 3.36E-07
LOC_Os11g10850.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.388; most accessible tissue: Zhenshan97 flag leaf, score: 96.051
vg1105978762 (J) chr11 5978762 G T 67.70% 0.00% T -> G NA
LOC_Os11g10850.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.675; most accessible tissue: Zhenshan97 flag leaf, score: 96.532
vg1105978811 (J) chr11 5978811 G T 93.00% 0.00% G -> T,A NA
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g10850.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.616; most accessible tissue: Zhenshan97 flag leaf, score: 97.172
vg1105978826 (J) chr11 5978826 C T 98.50% 0.00% C -> T NA
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.834; most accessible tissue: Zhenshan97 flag leaf, score: 97.166
vg1105978833 (J) chr11 5978833 G C 52.30% 0.00% C -> G
mr1216 (Ind_All); LR P-value: 3.28E-07;
mr1521 (All); LR P-value: 4.66E-13;
mr1740 (Jap_All); LR P-value: 4.33E-06;
mr1835 (All); LR P-value: 1.51E-07
LOC_Os11g10850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.573; most accessible tissue: Zhenshan97 flag leaf, score: 96.977
vg1105978897 (J) chr11 5978897 T C 53.20% 0.00% C -> T
mr1216 (Ind_All); LR P-value: 5.06E-07;
mr1521 (All); LR P-value: 3.61E-13;
mr1740 (Jap_All); LR P-value: 4.33E-06;
mr1835 (All); LR P-value: 1.93E-07;
mr1648_2 (All); LR P-value: 9.49E-06
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.300; most accessible tissue: Zhenshan97 flag leaf, score: 96.887
vg1105978899 (J) chr11 5978899 G C 53.20% 0.00% C -> G
mr1216 (Ind_All); LR P-value: 1.36E-06;
mr1521 (All); LR P-value: 3.60E-13;
mr1740 (Jap_All); LR P-value: 4.33E-06;
mr1835 (All); LR P-value: 3.24E-07;
mr1648_2 (All); LR P-value: 9.07E-06
LOC_Os11g10850.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.302; most accessible tissue: Zhenshan97 flag leaf, score: 96.894
vg1105978901 (J) chr11 5978901 C T 88.40% 0.00% C -> T NA
LOC_Os11g10850.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.311; most accessible tissue: Zhenshan97 flag leaf, score: 96.970
vg1105978902 (J) chr11 5978902 G C 98.50% 0.00% G -> C NA
LOC_Os11g10850.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.311; most accessible tissue: Zhenshan97 flag leaf, score: 96.970
vg1105978978 (J) chr11 5978978 C A 52.80% 0.00% A -> C
mr1216 (Ind_All); LR P-value: 8.16E-07;
mr1521 (All); LR P-value: 4.73E-13;
mr1740 (Jap_All); LR P-value: 4.33E-06;
mr1835 (All); LR P-value: 1.83E-07;
mr1648_2 (All); LR P-value: 2.45E-06
LOC_Os11g10850.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.168; most accessible tissue: Zhenshan97 flag leaf, score: 95.535
vg1105978986 (J) chr11 5978986 G GA 69.30% 16.53% G -> GACTACGAGC TAATTAATAT GGCTGTGCAT CCACTA,GA, GACTACGAGC TAATTAATAT GGCTGTGCAT CCACTACTAC AAAA NA
LOC_Os11g10860.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10840.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850-LOC_Os11g10860 Alt: GA| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10860.1 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10840.1 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850.1 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850-LOC_Os11g10860 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTA| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g10860.1 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10840.1 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850.1 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g10850-LOC_Os11g10860 Alt: GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367