47 variations found. Os02g0523500/LOC_Os02g32350 (TUDOR protein with multiple SNc domains; putative; expressed), ranging from 19,098,853 bp to 19,105,533 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g32350 | TUDOR protein with multiple SNc domains, putative, expressed; RAP ID: Os02g0523500; MSU ID: LOC_Os02g32350 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os02g32350 | Os02g0523500 | Rp120 | cytoskeleton-associated 120 kDa RNA-binding protein | AY320036. | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0219102132 (J) | chr02 | 19102132 | C | T | 96.10% | 0.00% | C -> T | NA |
|
| STR0219104641 (J) | chr02 | 19104641 | A | AC | 95.60% | 0.00% | A -> AC | NA |
|
| STR0219105159 (J) | chr02 | 19105159 | GGCGGCG GCGGGA | GCCGGCG GCGGGA | 91.50% | 0.00% | GGCGGCGGCG GGA -> GCCGGCGGCG GGA | NA |
|
| STR0219105504 (J) | chr02 | 19105504 | CCTCCCT CC | CCTCCCT CCCT | 94.70% | 0.00% | CCTCCCTCC -> CCTCCCTCCC T | NA |
|
| vg0219098889 (J) | chr02 | 19098889 | CTTTAAG TTCAATC CTGAATT | C | 87.50% | 0.00% | CTTTAAGTTC AATCCTGAAT T -> C | NA |
LOC_Os02g32350.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.850; most accessible tissue: Minghui63 flower, score: 95.731 |
| vg0219099131 (J) | chr02 | 19099131 | CTT | C | 54.90% | 0.21% | CTT -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.782; most accessible tissue: Minghui63 flower, score: 95.471 |
| vg0219099265 (J) | chr02 | 19099265 | C | A | 92.30% | 0.00% | C -> A | NA |
LOC_Os02g32350.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g32350.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.968; most accessible tissue: Minghui63 flower, score: 94.389 |
| vg0219099437 (J) | chr02 | 19099437 | A | G | 99.20% | 0.00% | A -> G | NA |
LOC_Os02g32340.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g32350.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os02g32350.2 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.612; most accessible tissue: Minghui63 flower, score: 92.602 |
| vg0219099880 (J) | chr02 | 19099880 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os02g32350.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g32350.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 78.340; most accessible tissue: Minghui63 flower, score: 88.486 |
| vg0219099918 (J) | chr02 | 19099918 | G | C | 92.30% | 0.00% | G -> C | NA |
LOC_Os02g32350.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g32350.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 75.151; most accessible tissue: Minghui63 flower, score: 86.932 |
| vg0219100083 (J) | chr02 | 19100083 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g32340.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.777; most accessible tissue: Minghui63 flower, score: 80.339 |
| vg0219100123 (J) | chr02 | 19100123 | T | C | 54.80% | 0.25% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.833; most accessible tissue: Minghui63 flower, score: 76.594 |
|
| vg0219100137 (J) | chr02 | 19100137 | G | C | 92.30% | 0.00% | G -> C | NA |
LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.677; most accessible tissue: Zhenshan97 flower, score: 75.194 |
| vg0219100224 (J) | chr02 | 19100224 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g32340.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g32350.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os02g32350.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 56.097; most accessible tissue: Callus, score: 76.154 |
| vg0219100336 (J) | chr02 | 19100336 | A | G | 97.70% | 0.00% | A -> G | NA |
LOC_Os02g32340.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.727; most accessible tissue: Minghui63 flower, score: 71.157 |
| vg0219100431 (J) | chr02 | 19100431 | C | T | 98.40% | 0.00% | C -> T | NA |
LOC_Os02g32340.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.101; most accessible tissue: Callus, score: 73.155 |
| vg0219100446 (J) | chr02 | 19100446 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os02g32340.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g32350.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os02g32350.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.284; most accessible tissue: Callus, score: 73.155 |
| vg0219100616 (J) | chr02 | 19100616 | G | A | 52.50% | 0.28% | A -> G |
LOC_Os02g32340.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.299; most accessible tissue: Minghui63 flower, score: 77.024 |
|
| vg0219100746 (J) | chr02 | 19100746 | G | T | 99.50% | 0.00% | G -> T | NA |
LOC_Os02g32340.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g32350.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os02g32350.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.834; most accessible tissue: Zhenshan97 flower, score: 78.132 |
| vg0219100806 (J) | chr02 | 19100806 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os02g32350.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os02g32350.2 Alt: C| missense_variant MODERATE(snpEff) LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.224; most accessible tissue: Zhenshan97 flower, score: 79.691 |
| vg0219100892 (J) | chr02 | 19100892 | T | A | 52.50% | 0.32% | A -> T |
LOC_Os02g32350.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os02g32350.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os02g32350.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g32350.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 61.931; most accessible tissue: Zhenshan97 flower, score: 78.677 |
|
| vg0219101073 (J) | chr02 | 19101073 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os02g32350.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os02g32350.2 Alt: C| synonymous_variant LOW(snpEff) LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.864; most accessible tissue: Zhenshan97 flower, score: 80.613 |
| vg0219101129 (J) | chr02 | 19101129 | C | G | 92.50% | 0.00% | C -> G | NA |
LOC_Os02g32340.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g32350.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g32350.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.946; most accessible tissue: Zhenshan97 flower, score: 81.724 |
| vg0219101372 (J) | chr02 | 19101372 | T | C | 99.50% | 0.00% | T -> C | NA |
LOC_Os02g32340.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g32350.1 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os02g32350.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.788; most accessible tissue: Minghui63 flag leaf, score: 82.750 |
| vg0219101575 (J) | chr02 | 19101575 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os02g32350.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g32350.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 72.164; most accessible tissue: Minghui63 flag leaf, score: 82.053 |
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