27 variations found. Os04g0424200/LOC_Os04g34670 (tRNA-splicing endonuclease positive effector-related; putative; expressed), ranging from 20,967,160 bp to 20,973,125 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g34670 | tRNA-splicing endonuclease positive effector-related, putative, expressed; RAP ID: Os04g0424200; MSU ID: LOC_Os04g34670 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967182 (J) | chr04 | 20967182 | G | A | 92.10% | 1.12% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 27.773; most accessible tissue: Minghui63 panicle, score: 42.799 |
| vg0420967202 (J) | chr04 | 20967202 | CG | Unkown | 27.00% | 54.63% | C -> CG | NA |
LOC_Os04g34670.1 Alt: CG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 30.069; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0420967226 (J) | chr04 | 20967226 | G | C | 1.70% | 50.78% | C -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34650.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 30.209; most accessible tissue: Zhenshan97 panicle, score: 54.901 |
| vg0420967231 (J) | chr04 | 20967231 | C | Unkown | 12.40% | 59.71% | A -> C | NA |
LOC_Os04g34670.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 30.328; most accessible tissue: Zhenshan97 panicle, score: 54.901 |
| vg0420967277 (J) | chr04 | 20967277 | T | G | 54.80% | 35.25% | T -> G |
|
LOC_Os04g34670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g34670.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 32.621; most accessible tissue: Zhenshan97 panicle, score: 52.263 |
| vg0420967319 (J) | chr04 | 20967319 | C | T | 57.10% | 13.86% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.430; most accessible tissue: Zhenshan97 panicle, score: 65.386 |
| vg0420967349 (J) | chr04 | 20967349 | C | CACCATG G | 88.40% | 3.26% | C -> CACCATGG,T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: CACCATGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: CACCATGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.666; most accessible tissue: Zhenshan97 panicle, score: 72.468 |
| vg0420967437 (J) | chr04 | 20967437 | C | A | 56.70% | 4.61% | C -> A | NA |
LOC_Os04g34670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g34670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 44.296; most accessible tissue: Zhenshan97 panicle, score: 73.605 |
| vg0420967517 (J) | chr04 | 20967517 | C | T | 83.60% | 11.64% | C -> T | NA |
LOC_Os04g34670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g34670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 53.716; most accessible tissue: Zhenshan97 panicle, score: 84.824 |
| vg0420967564 (J) | chr04 | 20967564 | C | T | 75.90% | 9.75% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.574; most accessible tissue: Zhenshan97 panicle, score: 85.254 |
| vg0420967601 (J) | chr04 | 20967601 | AGTGT | A | 57.90% | 1.52% | AGTGT -> A,AGT,AGTG TGT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34650.1 Alt: AGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: AGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34650.1 Alt: AGTGTGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: AGTGTGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.359; most accessible tissue: Zhenshan97 panicle, score: 82.888 |
| vg0420967637 (J) | chr04 | 20967637 | C | T | 98.30% | 0.13% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 |
| vg0420967638 (J) | chr04 | 20967638 | G | Unkown | 97.90% | 1.61% | G -> T | NA |
LOC_Os04g34650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g34670.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.836; most accessible tissue: Zhenshan97 panicle, score: 82.336 |
| vg0420968005 (J) | chr04 | 20968005 | G | GTGTAAC ACCCTGA AAATTCA ACCAGCG AAAA | 97.60% | 1.42% | G -> GTGTAA,GTG TAACAC,GTG TAACACCCTG AAAATTCAAC CAGCGAAAA, GTGTAACACC CTGAAAATTC AACCAGCGAA AACAAAACTC TAAAAATACG GGCTTT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: GTGTAACACCCTGAAAATTCAACCAGCGAAAACAAAACTCTAAAAATACGGGCTTT| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g34670.1 Alt: GTGTAACACCCTGAAAATTCAACCAGCGAAAACAAAACTCTAAAAATACGGGCTTT| intron_variant MODIFIER(snpEff) LOC_Os04g34650.1 Alt: GTGTAACACCCTGAAAATTCAACCAGCGAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: GTGTAACACCCTGAAAATTCAACCAGCGAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34650.1 Alt: GTGTAACAC| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g34670.1 Alt: GTGTAACAC| intron_variant MODIFIER(snpEff) LOC_Os04g34650.1 Alt: GTGTAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: GTGTAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0420968033 (J) | chr04 | 20968033 | C | A | 96.40% | 2.20% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 18.058; most accessible tissue: Zhenshan97 flower, score: 34.767 |
| vg0420968069 (J) | chr04 | 20968069 | A | C | 56.10% | 30.60% | A -> C |
|
LOC_Os04g34650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 17.193; most accessible tissue: Zhenshan97 flower, score: 34.767 |
| vg0420969506 (J) | chr04 | 20969506 | CTG | C | 56.70% | 40.39% | CTG -> C | NA |
LOC_Os04g34650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.444; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0420970814 (J) | chr04 | 20970814 | A | G | 69.10% | 29.37% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.675; most accessible tissue: Zhenshan97 panicle, score: 24.575 |
| vg0420971154 (J) | chr04 | 20971154 | T | G | 66.30% | 31.08% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 15.520; most accessible tissue: Zhenshan97 root, score: 50.453 |
| vg0420971503 (J) | chr04 | 20971503 | C | T | 58.10% | 38.87% | C -> T | NA |
LOC_Os04g34670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g34670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 8.596; most accessible tissue: Zhenshan97 flower, score: 19.853 |
| vg0420971615 (J) | chr04 | 20971615 | G | A | 65.70% | 30.79% | G -> A | NA |
LOC_Os04g34670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g34670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.644; most accessible tissue: Zhenshan97 flower, score: 15.748 |
| vg0420972028 (J) | chr04 | 20972028 | G | A | 38.10% | 41.98% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34680.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.411; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0420972175 (J) | chr04 | 20972175 | T | A | 57.70% | 39.86% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34680.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 16.058; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0420972685 (J) | chr04 | 20972685 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os04g34670.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 6.298; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg0420972720 (J) | chr04 | 20972720 | C | T | 95.90% | 0.06% | C -> T | NA |
LOC_Os04g34670.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g34670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.828; most accessible tissue: Zhenshan97 flower, score: 14.863 |
| vg0420972884 (J) | chr04 | 20972884 | A | T | 54.90% | 18.24% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34680.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 22.991; most accessible tissue: Zhenshan97 root, score: 41.416 |
| vg0420973001 (J) | chr04 | 20973001 | A | G | 48.60% | 40.92% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g34670.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g34680.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.910; most accessible tissue: Zhenshan97 flower, score: 74.953 |