18 variations found. Os01g0136100/LOC_Os01g04370 (hsp20%2Falpha crystallin family protein; putative; expressed), ranging from 1,948,736 bp to 1,949,587 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g04370 | hsp20/alpha crystallin family protein, putative, expressed; RAP ID: Os01g0136100; MSU ID: LOC_Os01g04370 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os01g04370 | Os01g0136100 | Oshsp16.9A, OsHsp16.9A, HSP16.9A, OsHSP16.9A-CI | 16.9 kDa class I heat shock protein 1, 16.9 kDa heat shock protein 1 | small heat shock protein. P27777. M80938. X60820. | HSP16.9A | 16.9 KDA CLASS I HEAT SHOCK PROTEIN 1 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0101948741 (J) | chr01 | 1948741 | C | T | 96.00% | 0.00% | C -> T | NA |
LOC_Os01g04370.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.981; most accessible tissue: Callus, score: 80.008 |
| vg0101948831 (J) | chr01 | 1948831 | T | A | 58.90% | 0.23% | A -> T |
LOC_Os01g04370.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 67.925; most accessible tissue: Zhenshan97 flower, score: 82.111 |
|
| vg0101948858 (J) | chr01 | 1948858 | A | C | 99.50% | 0.00% | A -> C | NA |
LOC_Os01g04370.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.052; most accessible tissue: Zhenshan97 flower, score: 82.359 |
| vg0101948890 (J) | chr01 | 1948890 | C | G | 78.00% | 0.00% | G -> C | NA |
LOC_Os01g04370.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.871; most accessible tissue: Zhenshan97 flower, score: 83.499 |
| vg0101948905 (J) | chr01 | 1948905 | C | T | 91.90% | 0.00% | C -> T |
LOC_Os01g04370.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.965; most accessible tissue: Zhenshan97 flower, score: 84.313 |
|
| vg0101949068 (J) | chr01 | 1949068 | G | A | 58.80% | 0.23% | A -> G |
LOC_Os01g04370.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g04370.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 74.786; most accessible tissue: Zhenshan97 flower, score: 88.571 |
|
| vg0101949113 (J) | chr01 | 1949113 | G | C | 91.40% | 0.00% | G -> C | NA |
LOC_Os01g04370.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.604; most accessible tissue: Zhenshan97 flower, score: 87.106 |
| vg0101949130 (J) | chr01 | 1949130 | G | T | 51.10% | 0.00% | T -> G |
mr1184_2 (All); LR P-value: 2.52E-08;
mr1278_2 (All); LR P-value: 2.33E-07; mr1329_2 (All); LR P-value: 3.56E-06; mr1418_2 (All); LR P-value: 6.79E-07; mr1488_2 (All); LR P-value: 2.16E-06; mr1524_2 (All); LR P-value: 2.88E-07; mr1683_2 (All); LR P-value: 2.25E-09; mr1838_2 (All); LR P-value: 5.22E-13; mr1982_2 (All); LR P-value: 7.10E-06 |
LOC_Os01g04370.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.755; most accessible tissue: Zhenshan97 flower, score: 86.841 |
| vg0101949212 (J) | chr01 | 1949212 | C | G | 62.70% | 0.23% | G -> C | NA |
LOC_Os01g04370.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g04370.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 69.879; most accessible tissue: Minghui63 panicle, score: 90.184 |
| vg0101949236 (J) | chr01 | 1949236 | T | C | 95.60% | 2.75% | T -> C | NA |
LOC_Os01g04370.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g04370.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 69.797; most accessible tissue: Minghui63 panicle, score: 91.586 |
| vg0101949269 (J) | chr01 | 1949269 | G | C | 95.60% | 2.77% | G -> C | NA |
LOC_Os01g04370.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g04370.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 70.540; most accessible tissue: Minghui63 panicle, score: 92.666 |
| vg0101949302 (J) | chr01 | 1949302 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g04370.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g04360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g04380.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.620; most accessible tissue: Minghui63 panicle, score: 92.928 |
| vg0101949308 (J) | chr01 | 1949308 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os01g04370.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.158; most accessible tissue: Minghui63 panicle, score: 92.928 |
| vg0101949388 (J) | chr01 | 1949388 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os01g04370.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 71.085; most accessible tissue: Minghui63 panicle, score: 94.794 |
| vg0101949422 (J) | chr01 | 1949422 | T | G | 99.90% | 0.00% | T -> G | NA |
LOC_Os01g04370.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os01g04360.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g04380.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.996; most accessible tissue: Minghui63 panicle, score: 96.507 |
| vg0101949468 (J) | chr01 | 1949468 | G | T | 67.40% | 0.02% | T -> G,A | NA |
LOC_Os01g04370.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04370.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04360.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.536; most accessible tissue: Minghui63 panicle, score: 97.163 |
| vg0101949520 (J) | chr01 | 1949520 | T | C | 77.30% | 0.00% | C -> T | NA |
LOC_Os01g04370.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g04360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g04380.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.161; most accessible tissue: Minghui63 panicle, score: 97.736 |
| STR0101948902 (J) | chr01 | 1948902 | CAGC | CAGT | 95.30% | 0.00% | CAGC -> CAGT | NA |
|