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Search Results:

22 variations found. Os03g0271300/LOC_Os03g16450 (pentatricopeptide; putative; expressed), ranging from 9,074,312 bp to 9,076,863 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os03g16450 pentatricopeptide, putative, expressed; RAP ID: Os03g0271300; MSU ID: LOC_Os03g16450

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
vg0309074442 (J) chr03 9074442 G A 98.70% 0.00% G -> A NA
LOC_Os03g16450.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.717; most accessible tissue: Zhenshan97 flag leaf, score: 97.759
vg0309074552 (J) chr03 9074552 T C 50.30% 0.06% T -> C
mr1188 (Ind_All); LR P-value: 5.26E-06;
mr1565 (All); LR P-value: 6.34E-11;
mr1565_2 (All); LR P-value: 1.98E-10;
mr1574_2 (All); LR P-value: 8.03E-06
LOC_Os03g16450.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g16450.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 96.737; most accessible tissue: Zhenshan97 flag leaf, score: 98.491
vg0309074681 (J) chr03 9074681 C T 50.40% 0.00% C -> T
mr1188 (All); LR P-value: 5.23E-11;
mr1188 (Ind_All); LR P-value: 1.48E-06;
mr1231 (Ind_All); LR P-value: 2.57E-06;
mr1565 (All); LR P-value: 1.28E-10;
mr1347_2 (Ind_All); LR P-value: 1.02E-06;
mr1574_2 (All); LR P-value: 6.43E-06
LOC_Os03g16450.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.324; most accessible tissue: Zhenshan97 flag leaf, score: 98.634
vg0309075044 (J) chr03 9075044 A T 99.80% 0.00% A -> T NA
LOC_Os03g16450.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g16470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16440.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16460.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 93.077; most accessible tissue: Zhenshan97 flag leaf, score: 96.701
vg0309075492 (J) chr03 9075492 G A 79.20% 0.00% G -> A NA
LOC_Os03g16450.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.922; most accessible tissue: Zhenshan97 young leaf, score: 96.297
vg0309075535 (J) chr03 9075535 T C 99.00% 0.00% T -> C NA
LOC_Os03g16450.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 93.079; most accessible tissue: Zhenshan97 young leaf, score: 96.443
vg0309075780 (J) chr03 9075780 T C 50.30% 0.72% T -> C
mr1188 (Ind_All); LR P-value: 2.89E-06;
mr1231 (Ind_All); LR P-value: 2.87E-06;
mr1565 (All); LR P-value: 4.68E-11;
mr1347_2 (Ind_All); LR P-value: 7.03E-07;
mr1565_2 (All); LR P-value: 1.42E-10;
mr1574_2 (All); LR P-value: 5.42E-06
LOC_Os03g16450.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g16450.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 92.665; most accessible tissue: Zhenshan97 young leaf, score: 95.514
vg0309075823 (J) chr03 9075823 G C 99.40% 0.00% G -> C NA
LOC_Os03g16450.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g16460.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g16470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16440.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 91.968; most accessible tissue: Zhenshan97 young leaf, score: 95.059
vg0309075889 (J) chr03 9075889 T G 99.90% 0.00% T -> G NA
LOC_Os03g16450.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g16460.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g16470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16440.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 90.161; most accessible tissue: Zhenshan97 young leaf, score: 94.425
vg0309075933 (J) chr03 9075933 A T 97.00% 0.00% A -> T NA
LOC_Os03g16450.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.539; most accessible tissue: Zhenshan97 young leaf, score: 92.356
vg0309076029 (J) chr03 9076029 C T 99.50% 0.00% C -> T NA
LOC_Os03g16450.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.557; most accessible tissue: Zhenshan97 flower, score: 90.115
vg0309076059 (J) chr03 9076059 T C 50.30% 0.06% T -> C
mr1188 (Ind_All); LR P-value: 2.97E-06;
mr1231 (Ind_All); LR P-value: 2.99E-06;
mr1565 (All); LR P-value: 3.44E-11;
mr1347_2 (Ind_All); LR P-value: 1.07E-06;
mr1565_2 (All); LR P-value: 7.98E-11;
mr1574_2 (All); LR P-value: 2.17E-06
LOC_Os03g16450.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 86.858; most accessible tissue: Zhenshan97 flower, score: 89.076
vg0309076080 (J) chr03 9076080 A C 94.10% 0.00% A -> C
mr1157 (All); LR P-value: 7.55E-08;
mr1244 (All); LR P-value: 5.26E-22;
mr1328 (All); LR P-value: 5.19E-08;
mr1442 (All); LR P-value: 1.60E-08;
mr1446 (All); LR P-value: 1.93E-09;
mr1499 (All); LR P-value: 5.18E-12;
mr1612 (All); LR P-value: 5.84E-11;
mr1706 (All); LR P-value: 5.32E-07;
mr1735 (All); LR P-value: 9.57E-08;
mr1858 (All); LR P-value: 9.15E-27;
mr1859 (All); LR P-value: 8.41E-27;
mr1989 (All); LR P-value: 8.81E-10
LOC_Os03g16450.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.883; most accessible tissue: Zhenshan97 flag leaf, score: 90.945
vg0309076182 (J) chr03 9076182 C G 50.30% 0.47% C -> G
mr1188 (Ind_All); LR P-value: 2.89E-06;
mr1231 (Ind_All); LR P-value: 2.87E-06;
mr1565 (All); LR P-value: 4.68E-11;
mr1347_2 (Ind_All); LR P-value: 7.03E-07;
mr1565_2 (All); LR P-value: 1.42E-10;
mr1574_2 (All); LR P-value: 5.42E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g16450.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.124; most accessible tissue: Zhenshan97 panicle, score: 90.849
vg0309076322 (J) chr03 9076322 T C 96.90% 0.00% T -> C NA
LOC_Os03g16450.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.590; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg0309076333 (J) chr03 9076333 T G 50.20% 0.32% T -> G
mr1188 (Ind_All); LR P-value: 2.89E-06;
mr1231 (Ind_All); LR P-value: 2.87E-06;
mr1565 (All); LR P-value: 4.68E-11;
mr1347_2 (Ind_All); LR P-value: 7.03E-07;
mr1565_2 (All); LR P-value: 1.42E-10;
mr1574_2 (All); LR P-value: 5.42E-06
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g16450.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16460.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16470.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g16440.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.927; most accessible tissue: Zhenshan97 panicle, score: 90.268
vg0309076351 (J) chr03 9076351 C T 99.90% 0.00% C -> T NA
LOC_Os03g16460.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os03g16450.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g16470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16440.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 84.725; most accessible tissue: Zhenshan97 panicle, score: 90.061
vg0309076449 (J) chr03 9076449 T C 50.30% 0.36% T -> C
mr1188 (Ind_All); LR P-value: 2.99E-06;
mr1231 (Ind_All); LR P-value: 4.65E-06;
mr1565 (All); LR P-value: 3.76E-11;
mr1565_2 (All); LR P-value: 7.56E-11;
mr1574_2 (All); LR P-value: 3.54E-06
LOC_Os03g16460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g16460.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.188; most accessible tissue: Zhenshan97 panicle, score: 92.270
vg0309076729 (J) chr03 9076729 T C 99.40% 0.00% T -> C NA
LOC_Os03g16460.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g16450.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g16470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g16440.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 83.673; most accessible tissue: Zhenshan97 young leaf, score: 91.069
vg0309076778 (J) chr03 9076778 A T 57.00% 0.40% A -> T
mr1174 (All); LR P-value: 1.29E-09;
mr1188 (Ind_All); LR P-value: 2.69E-06;
mr1542 (Ind_All); LR P-value: 4.41E-06;
mr1561 (All); LR P-value: 1.44E-06;
mr1565 (All); LR P-value: 1.55E-11;
mr1657 (All); LR P-value: 2.09E-11;
mr1875 (All); LR P-value: 4.82E-06;
mr1929 (All); LR P-value: 2.44E-08;
mr1174_2 (All); LR P-value: 2.99E-11;
mr1347_2 (All); LR P-value: 4.25E-08;
mr1347_2 (Ind_All); LR P-value: 3.09E-07;
mr1542_2 (Ind_All); LR P-value: 6.15E-06;
mr1561_2 (All); LR P-value: 8.24E-06;
mr1565_2 (All); LR P-value: 4.08E-12;
mr1908_2 (All); LR P-value: 6.86E-06
LOC_Os03g16460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g16460.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 81.501; most accessible tissue: Zhenshan97 young leaf, score: 89.666
vg0309076843 (J) chr03 9076843 T C 52.30% 0.53% C -> T
mr1188 (Ind_All); LR P-value: 3.01E-06;
mr1231 (Ind_All); LR P-value: 5.58E-06;
mr1565 (All); LR P-value: 2.75E-11;
mr1347_2 (Ind_All); LR P-value: 7.18E-07;
mr1565_2 (All); LR P-value: 1.11E-11
LOC_Os03g16460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g16460.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 78.238; most accessible tissue: Zhenshan97 young leaf, score: 87.584
STR0309076080 (J) chr03 9076080 A C 98.20% 0.00% A -> C NA