86 variations found. Os01g0171000/LOC_Os01g07630 (BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor; putative; expressed), ranging from 3,667,438 bp to 3,673,065 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g07630 | BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, putative, expressed; RAP ID: Os01g0171000; MSU ID: LOC_Os01g07630 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os01g07630 | Os01g0171000 | OsSERL5 | BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase, SERK-like gene 5 | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0103671422 (J) | chr01 | 3671422 | TTACTGA CTTG | TTACTTA CTTG | 48.20% | 0.00% | TTACTTACTT G -> TTACTGACTT G | NA |
|
| STR0103672821 (J) | chr01 | 3672821 | G | GCAGCTG | 72.00% | 0.00% | GCAGCTG -> G | NA |
|
| vg0103667515 (J) | chr01 | 3667515 | CT | C | 58.30% | 0.06% | C -> CT,CTT | NA |
LOC_Os01g07630.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07620.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07610.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07620.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07610.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.412; most accessible tissue: Callus, score: 90.028 |
| vg0103667694 (J) | chr01 | 3667694 | C | T | 54.80% | 0.17% | C -> T |
LOC_Os01g07630.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 65.364; most accessible tissue: Callus, score: 85.211 |
|
| vg0103667732 (J) | chr01 | 3667732 | A | C | 99.20% | 0.00% | A -> C | NA |
LOC_Os01g07630.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07620.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07610.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.479; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg0103667806 (J) | chr01 | 3667806 | G | C | 66.60% | 0.00% | C -> G |
LOC_Os01g07630.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.034; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
|
| vg0103667809 (J) | chr01 | 3667809 | G | A | 66.60% | 0.00% | A -> G |
LOC_Os01g07630.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.395; most accessible tissue: Zhenshan97 panicle, score: 85.665 |
|
| vg0103667842 (J) | chr01 | 3667842 | C | T | 80.00% | 0.11% | C -> T |
mr1248 (Jap_All); LR P-value: 1.13E-08;
mr1676 (Ind_All); LR P-value: 1.93E-06; mr1746 (Jap_All); LR P-value: 1.76E-07; mr1769 (Jap_All); LR P-value: 2.15E-14; mr1389_2 (Ind_All); LR P-value: 3.81E-06; mr1553_2 (Jap_All); LR P-value: 8.32E-06; mr1769_2 (Jap_All); LR P-value: 1.06E-14; mr1817_2 (Jap_All); LR P-value: 1.48E-07 |
LOC_Os01g07630.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g07630.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.868; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
| vg0103667899 (J) | chr01 | 3667899 | G | A | 54.80% | 0.11% | G -> A |
LOC_Os01g07630.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g07630.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 62.684; most accessible tissue: Zhenshan97 panicle, score: 86.432 |
|
| vg0103668168 (J) | chr01 | 3668168 | A | G | 66.10% | 0.00% | G -> A |
LOC_Os01g07620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.108; most accessible tissue: Zhenshan97 panicle, score: 78.302 |
|
| vg0103668330 (J) | chr01 | 3668330 | C | CA | 99.80% | 0.00% | C -> CA | NA |
LOC_Os01g07620.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.053; most accessible tissue: Minghui63 flower, score: 72.895 |
| vg0103668341 (J) | chr01 | 3668341 | C | A | 89.90% | 0.06% | C -> A |
LOC_Os01g07620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 47.422; most accessible tissue: Minghui63 flower, score: 72.332 |
|
| vg0103668423 (J) | chr01 | 3668423 | A | AAG | 99.20% | 0.00% | A -> AAG | NA |
LOC_Os01g07620.1 Alt: AAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: AAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.591; most accessible tissue: Minghui63 flower, score: 70.218 |
| vg0103668424 (J) | chr01 | 3668424 | C | CTCTA | 99.20% | 0.00% | C -> CTCTA | NA |
LOC_Os01g07620.1 Alt: CTCTA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: CTCTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: CTCTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.490; most accessible tissue: Minghui63 flower, score: 69.893 |
| vg0103668427 (J) | chr01 | 3668427 | A | AC | 99.20% | 0.00% | A -> AC | NA |
LOC_Os01g07620.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: AC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: AC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.500; most accessible tissue: Callus, score: 75.169 |
| vg0103668428 (J) | chr01 | 3668428 | G | GGACGAA ACAAA | 99.20% | 0.00% | G -> GGACGAAACA AA | NA |
LOC_Os01g07620.1 Alt: GGACGAAACAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: GGACGAAACAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: GGACGAAACAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.500; most accessible tissue: Callus, score: 75.169 |
| vg0103668429 (J) | chr01 | 3668429 | T | A | 99.20% | 0.00% | T -> A | NA |
LOC_Os01g07620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.654; most accessible tissue: Callus, score: 75.169 |
| vg0103668453 (J) | chr01 | 3668453 | T | C | 74.10% | 0.00% | C -> T | NA |
LOC_Os01g07620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.387; most accessible tissue: Callus, score: 75.169 |
| vg0103668543 (J) | chr01 | 3668543 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os01g07620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.367; most accessible tissue: Callus, score: 75.169 |
| vg0103668553 (J) | chr01 | 3668553 | T | C | 91.20% | 0.00% | T -> C |
LOC_Os01g07620.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.675; most accessible tissue: Callus, score: 75.169 |
|
| vg0103668568 (J) | chr01 | 3668568 | A | T | 91.10% | 0.00% | A -> T |
LOC_Os01g07620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.213; most accessible tissue: Callus, score: 75.169 |
|
| vg0103668583 (J) | chr01 | 3668583 | G | GA | 79.10% | 0.00% | G -> GA | NA |
LOC_Os01g07620.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.186; most accessible tissue: Minghui63 flower, score: 68.171 |
| vg0103668613 (J) | chr01 | 3668613 | A | G | 94.10% | 0.00% | A -> G |
mr1235 (Jap_All); LR P-value: 1.19E-10;
mr1746 (Jap_All); LR P-value: 1.11E-07; mr1769 (Jap_All); LR P-value: 6.84E-15; mr1951 (Jap_All); LR P-value: 1.08E-07; mr1039_2 (Jap_All); LR P-value: 6.36E-06; mr1510_2 (Jap_All); LR P-value: 4.51E-06; mr1632_2 (Jap_All); LR P-value: 8.00E-07; mr1769_2 (Jap_All); LR P-value: 3.85E-13; mr1849_2 (Jap_All); LR P-value: 5.87E-06; mr1905_2 (Jap_All); LR P-value: 1.24E-06; mr1916_2 (Jap_All); LR P-value: 4.48E-11 |
LOC_Os01g07620.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g07610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g07630.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.830; most accessible tissue: Zhenshan97 young leaf, score: 69.723 |
| vg0103668688 (J) | chr01 | 3668688 | C | T | 74.20% | 0.00% | T -> C | NA |
LOC_Os01g07630.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 55.716; most accessible tissue: Zhenshan97 panicle, score: 75.670 |
| vg0103668781 (J) | chr01 | 3668781 | C | T | 99.90% | 0.00% | C -> T,A | NA |
LOC_Os01g07630.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g07620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g07610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g07630.1 Alt: A| synonymous_variant LOW(snpEff) LOC_Os01g07620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g07610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.260; most accessible tissue: Zhenshan97 panicle, score: 74.671 |
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