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Search Results:

15 variations found. Os12g0424700/LOC_Os12g23700 (cyclin-dependent kinase G-2; putative; expressed), ranging from 13,444,610 bp to 13,445,594 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os12g23700 cyclin-dependent kinase G-2, putative, expressed; RAP ID: Os12g0424700; MSU ID: LOC_Os12g23700

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
vg1213444658 (J) chr12 13444658 A C 85.00% 0.06% C -> A
mr1023 (All); LR P-value: 8.96E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 6.39E-46;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 3.32E-11;
mr1308 (All); LR P-value: 7.71E-17;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 5.27E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 3.98E-16;
mr1023_2 (All); LR P-value: 1.30E-71;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 3.60E-15;
mr1079_2 (All); LR P-value: 1.59E-54;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1368_2 (All); LR P-value: 2.71E-32;
mr1471_2 (All); LR P-value: 3.11E-09;
mr1489_2 (All); LR P-value: 1.61E-77;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 1.07E-07;
mr1722_2 (All); LR P-value: 3.41E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 1.19E-12;
mr1942_2 (All); LR P-value: 1.15E-09
LOC_Os12g23700.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23700.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.780; most accessible tissue: Zhenshan97 root, score: 99.336
vg1213444668 (J) chr12 13444668 A G 70.80% 0.00% G -> A
mr1002 (All); LR P-value: 8.46E-08;
mr1023 (Jap_All); LR P-value: 8.50E-15;
mr1142 (Jap_All); LR P-value: 4.15E-14;
mr1178 (Jap_All); LR P-value: 3.26E-10;
mr1182 (All); LR P-value: 5.09E-13;
mr1207 (All); LR P-value: 5.95E-07;
mr1282 (All); LR P-value: 1.42E-10;
mr1308 (All); LR P-value: 5.70E-17;
mr1401 (Jap_All); LR P-value: 9.10E-07;
mr1563 (Jap_All); LR P-value: 1.01E-08;
mr1584 (Jap_All); LR P-value: 8.54E-07;
mr1606 (All); LR P-value: 3.57E-07;
mr1606 (Jap_All); LR P-value: 9.74E-07;
mr1607 (All); LR P-value: 1.07E-10;
mr1657 (Jap_All); LR P-value: 2.41E-06;
mr1658 (All); LR P-value: 8.62E-09;
mr1730 (All); LR P-value: 5.01E-10;
mr1778 (Jap_All); LR P-value: 2.81E-13;
mr1866 (All); LR P-value: 1.17E-08;
mr1942 (All); LR P-value: 4.63E-10;
mr1159_2 (All); LR P-value: 2.09E-07;
mr1189_2 (Jap_All); LR P-value: 1.17E-08;
mr1338_2 (Jap_All); LR P-value: 1.50E-08;
mr1368_2 (Jap_All); LR P-value: 1.29E-10;
mr1607_2 (All); LR P-value: 2.97E-08;
mr1778_2 (Jap_All); LR P-value: 6.97E-14;
mr1815_2 (All); LR P-value: 9.08E-07;
mr1860_2 (Jap_All); LR P-value: 2.42E-06;
mr1910_2 (All); LR P-value: 5.21E-06;
mr1942_2 (All); LR P-value: 6.76E-14
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.513; most accessible tissue: Zhenshan97 root, score: 99.160
vg1213444684 (J) chr12 13444684 C A 78.10% 0.00% C -> A NA
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 96.152; most accessible tissue: Zhenshan97 root, score: 99.132
vg1213444716 (J) chr12 13444716 C T 67.20% 0.00% C -> T
Spikelet_length (Ind_All); LR P-value: 5.28E-07;
mr1050 (Ind_All); LR P-value: 3.05E-06;
mr1308 (Ind_All); LR P-value: 5.35E-07;
mr1531 (All); LR P-value: 4.47E-13;
mr1707 (All); LR P-value: 1.07E-07;
mr1728 (All); LR P-value: 8.60E-07;
mr1860 (All); LR P-value: 5.48E-09;
mr1050_2 (All); LR P-value: 1.88E-10;
mr1050_2 (Ind_All); LR P-value: 3.07E-07;
mr1136_2 (Ind_All); LR P-value: 3.95E-06;
mr1272_2 (All); LR P-value: 2.69E-07;
mr1308_2 (Ind_All); LR P-value: 3.45E-06;
mr1361_2 (Ind_All); LR P-value: 6.32E-07;
mr1707_2 (All); LR P-value: 1.82E-08;
mr1728_2 (All); LR P-value: 2.65E-11;
mr1860_2 (All); LR P-value: 1.09E-09
LOC_Os12g23700.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.975; most accessible tissue: Zhenshan97 root, score: 98.940
vg1213444832 (J) chr12 13444832 G GGGC 84.40% 0.00% GGGC -> G NA
LOC_Os12g23700.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 90.969; most accessible tissue: Zhenshan97 root, score: 97.403
vg1213444941 (J) chr12 13444941 A G 85.10% 0.00% G -> A
mr1023 (All); LR P-value: 8.96E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 6.39E-46;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1182 (All); LR P-value: 3.32E-11;
mr1308 (All); LR P-value: 7.71E-17;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 5.27E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 3.98E-16;
mr1023_2 (All); LR P-value: 1.30E-71;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 3.60E-15;
mr1079_2 (All); LR P-value: 1.59E-54;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1368_2 (All); LR P-value: 2.71E-32;
mr1471_2 (All); LR P-value: 3.11E-09;
mr1489_2 (All); LR P-value: 1.61E-77;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 1.07E-07;
mr1722_2 (All); LR P-value: 3.41E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 1.19E-12;
mr1942_2 (All); LR P-value: 1.15E-09
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.735; most accessible tissue: Zhenshan97 root, score: 96.313
vg1213444950 (J) chr12 13444950 C T 87.20% 0.00% C -> T
mr1156 (Jap_All); LR P-value: 2.05E-06;
mr1177 (All); LR P-value: 1.60E-06;
mr1236 (All); LR P-value: 9.17E-09;
mr1236 (Jap_All); LR P-value: 1.08E-07;
mr1063_2 (Ind_All); LR P-value: 9.12E-08
LOC_Os12g23700.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.770; most accessible tissue: Zhenshan97 root, score: 96.303
vg1213445085 (J) chr12 13445085 G A 84.30% 0.57% A -> G NA
LOC_Os12g23700.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23700.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.875; most accessible tissue: Zhenshan97 root, score: 95.543
vg1213445088 (J) chr12 13445088 A G 84.10% 1.08% G -> A NA
LOC_Os12g23700.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.886; most accessible tissue: Zhenshan97 root, score: 95.543
vg1213445089 (J) chr12 13445089 C A 79.20% 0.30% C -> A NA
LOC_Os12g23700.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.772; most accessible tissue: Zhenshan97 root, score: 95.366
vg1213445153 (J) chr12 13445153 C T 84.40% 0.55% T -> C
mr1023 (All); LR P-value: 3.68E-61;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (All); LR P-value: 4.41E-46;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1308 (All); LR P-value: 1.00E-17;
mr1489 (All); LR P-value: 8.99E-69;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 1.54E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1959 (All); LR P-value: 2.19E-09;
mr1013_2 (All); LR P-value: 9.82E-16;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1031_2 (All); LR P-value: 2.37E-14;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1156_2 (All); LR P-value: 4.07E-18;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1368_2 (All); LR P-value: 1.56E-32;
mr1489_2 (All); LR P-value: 1.47E-76;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1722_2 (All); LR P-value: 4.35E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 5.86E-12
LOC_Os12g23700.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g23700.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 88.207; most accessible tissue: Zhenshan97 root, score: 95.656
vg1213445255 (J) chr12 13445255 G A 85.10% 0.00% A -> G
mr1023 (All); LR P-value: 9.22E-60;
mr1023 (Jap_All); LR P-value: 4.75E-15;
mr1079 (Jap_All); LR P-value: 7.22E-13;
mr1142 (Jap_All); LR P-value: 4.33E-14;
mr1178 (Jap_All); LR P-value: 6.35E-10;
mr1489 (Jap_All); LR P-value: 3.72E-14;
mr1491 (Jap_All); LR P-value: 3.63E-14;
mr1606 (All); LR P-value: 3.55E-08;
mr1606 (Jap_All); LR P-value: 2.32E-06;
mr1657 (Jap_All); LR P-value: 6.39E-06;
mr1778 (Jap_All); LR P-value: 3.17E-13;
mr1013_2 (All); LR P-value: 1.01E-15;
mr1023_2 (All); LR P-value: 1.29E-70;
mr1023_2 (Jap_All); LR P-value: 3.13E-16;
mr1079_2 (Jap_All); LR P-value: 2.03E-13;
mr1189_2 (Jap_All); LR P-value: 4.69E-08;
mr1338_2 (Jap_All); LR P-value: 2.18E-08;
mr1471_2 (All); LR P-value: 8.14E-09;
mr1489_2 (All); LR P-value: 1.66E-77;
mr1489_2 (Jap_All); LR P-value: 5.95E-15;
mr1606_2 (All); LR P-value: 9.75E-08;
mr1722_2 (All); LR P-value: 5.00E-12;
mr1778_2 (Jap_All); LR P-value: 1.78E-13;
mr1879_2 (All); LR P-value: 2.31E-12
LOC_Os12g23700.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.705; most accessible tissue: Zhenshan97 root, score: 95.969
vg1213445503 (J) chr12 13445503 C A 98.00% 0.00% C -> A NA
LOC_Os12g23700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.985; most accessible tissue: Zhenshan97 root, score: 96.814
vg1213445561 (J) chr12 13445561 C T 99.90% 0.00% C -> T NA
LOC_Os12g23700.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g23710.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os12g23690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.700; most accessible tissue: Zhenshan97 root, score: 96.814
STR1213444833 (J) chr12 13444833 GGCGGCG GC GGCGGCG GCGGC 64.00% 0.00% GGCGGCGGCG GC -> GGCGGCGGC NA