21 variations found. Os11g0136600/LOC_Os11g04170 (CAMK_CAMK_like.42 - CAMK includes calcium%2Fcalmodulin depedent protein kinases; expressed), ranging from 1,691,860 bp to 1,694,301 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g04170 | CAMK_CAMK_like.42 - CAMK includes calcium/calmodulin depedent protein kinases, expressed; RAP ID: Os11g0136600; MSU ID: LOC_Os11g04170 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os11g04170 | Os11g0136600 | OsCDPK25, OsCPK25 | calcium-dependent protein kinase | AC123528. | CDPK25 | CALCIUM-DEPENDENT PROTEIN KINASE 25 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101691860 (J) | chr11 | 1691860 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os11g04150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04170.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04160-LOC_Os11g04170 Alt: C| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.171; most accessible tissue: Zhenshan97 root, score: 82.361 |
| vg1101692021 (J) | chr11 | 1692021 | G | T | 99.20% | 0.00% | G -> T | NA |
LOC_Os11g04170.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 62.114; most accessible tissue: Minghui63 panicle, score: 74.563 |
| vg1101692044 (J) | chr11 | 1692044 | AGGCGGC GGCGACG GAAGCGG C | AGGC | 98.40% | 0.00% | AGGCGGCGGC GACGGAAGCG GC -> A,AGGC | NA |
LOC_Os11g04170.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g04170.1 Alt: AGGC| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 62.212; most accessible tissue: Zhenshan97 root, score: 74.877 |
| vg1101692318 (J) | chr11 | 1692318 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os11g04170.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.809; most accessible tissue: Zhenshan97 panicle, score: 77.482 |
| vg1101692327 (J) | chr11 | 1692327 | A | C | 99.00% | 0.00% | A -> C,G | NA |
LOC_Os11g04170.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os11g04150.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04174.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04170.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 |
| vg1101692470 (J) | chr11 | 1692470 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g04170.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g04150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04174.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.902; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
| vg1101692555 (J) | chr11 | 1692555 | G | A | 67.20% | 26.07% | G -> A | NA |
LOC_Os11g04170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g04170.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.420; most accessible tissue: Zhenshan97 panicle, score: 85.254 |
| vg1101692762 (J) | chr11 | 1692762 | G | A | 55.70% | 33.24% | G -> A,C | NA |
LOC_Os11g04170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g04170.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g04170.1 Alt: C| synonymous_variant LOW(snpEff) LOC_Os11g04150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.980; most accessible tissue: Zhenshan97 panicle, score: 87.451 |
| vg1101692786 (J) | chr11 | 1692786 | C | Unkown | 99.70% | 0.00% | C -> T | NA |
LOC_Os11g04170.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g04150.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04174.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.695; most accessible tissue: Zhenshan97 panicle, score: 87.451 |
| vg1101692944 (J) | chr11 | 1692944 | T | C | 99.00% | 0.00% | T -> C | NA |
LOC_Os11g04150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.091; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
| vg1101692951 (J) | chr11 | 1692951 | CT | C | 84.40% | 7.00% | CT -> C,CTT | NA |
LOC_Os11g04150.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)
LOC_Os11g04160.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04174.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04180.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04170.1 Alt: CTT| intron_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os11g04150.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.140; most accessible tissue: Zhenshan97 panicle, score: 86.788 |
| vg1101692965 (J) | chr11 | 1692965 | T | A | 98.60% | 0.28% | T -> A | NA |
LOC_Os11g04150.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 67.131; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
| vg1101693216 (J) | chr11 | 1693216 | T | C | 98.80% | 0.00% | T -> C | NA |
LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.465; most accessible tissue: Zhenshan97 panicle, score: 69.946 |
| vg1101693413 (J) | chr11 | 1693413 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os11g04160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04174.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.999; most accessible tissue: Zhenshan97 panicle, score: 59.590 |
| vg1101693429 (J) | chr11 | 1693429 | CTTAG | C | 56.10% | 28.61% | CTTAG -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.108; most accessible tissue: Zhenshan97 panicle, score: 61.671 |
| vg1101693431 (J) | chr11 | 1693431 | T | TC | 62.40% | 24.04% | T -> TC | NA |
LOC_Os11g04160.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04174.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 40.693; most accessible tissue: Zhenshan97 panicle, score: 65.386 |
| vg1101693521 (J) | chr11 | 1693521 | C | T | 55.20% | 33.96% | C -> T | NA |
LOC_Os11g04170.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g04170.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 37.008; most accessible tissue: Zhenshan97 root, score: 60.612 |
| vg1101693689 (J) | chr11 | 1693689 | G | T | 34.00% | 57.43% | G -> T,C | NA |
LOC_Os11g04160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g04174.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os11g04160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 |
| vg1101693903 (J) | chr11 | 1693903 | T | G | 67.00% | 27.40% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g04160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04170.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 28.150; most accessible tissue: Zhenshan97 root, score: 39.742 |
| vg1101694274 (J) | chr11 | 1694274 | A | G | 54.70% | 0.23% | A -> G |
mr1565 (All); LR P-value: 1.48E-10;
mr1904 (Ind_All); LR P-value: 2.64E-10; mr1170_2 (All); LR P-value: 1.06E-07; mr1184_2 (All); LR P-value: 1.89E-07; mr1278_2 (All); LR P-value: 6.23E-07; mr1329_2 (All); LR P-value: 3.83E-06; mr1418_2 (All); LR P-value: 1.75E-06; mr1420_2 (All); LR P-value: 8.84E-06; mr1488_2 (All); LR P-value: 1.42E-06; mr1508_2 (All); LR P-value: 2.04E-06; mr1524_2 (All); LR P-value: 4.10E-06; mr1556_2 (All); LR P-value: 6.72E-06; mr1683_2 (All); LR P-value: 2.81E-09; mr1779_2 (All); LR P-value: 3.77E-06; mr1838_2 (All); LR P-value: 6.43E-14; mr1992_2 (All); LR P-value: 3.28E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g04170.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04174.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g04180.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 25.671; most accessible tissue: Zhenshan97 root, score: 38.035 |
| STR1101692017 (J) | chr11 | 1692017 | AGCAG | AGCAT | 85.80% | 0.00% | AGCAG -> AGCAT | NA |
|