5 variations found. Os11g0114000/LOC_Os11g02260 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 642,576 bp to 642,981 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g02260 | zinc finger, C3HC4 type domain containing protein; RAP ID: Os11g0114000; MSU ID: LOC_Os11g02260 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100642618 (J) | chr11 | 642618 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g02260.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.767; most accessible tissue: Minghui63 young leaf, score: 99.507 |
| vg1100642837 (J) | chr11 | 642837 | G | A | 95.80% | 0.00% | G -> A | NA |
LOC_Os11g02260.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.993; most accessible tissue: Minghui63 young leaf, score: 99.668 |
| vg1100642844 (J) | chr11 | 642844 | G | T | 78.00% | 0.00% | G -> T | NA |
LOC_Os11g02260.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.919; most accessible tissue: Minghui63 young leaf, score: 99.661 |
| vg1100642947 (J) | chr11 | 642947 | TCGC | T | 78.20% | 6.86% | TCGC -> T | NA |
LOC_Os11g02260.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g02260.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.212; most accessible tissue: Minghui63 young leaf, score: 99.423 |
| vg1100642956 (J) | chr11 | 642956 | C | T | 78.70% | 6.94% | C -> T | NA |
LOC_Os11g02260.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g02260.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.155; most accessible tissue: Minghui63 young leaf, score: 99.406 |