66 variations found. Os03g0796900/LOC_Os03g58250 (bZIP transcription factor domain containing protein; expressed), ranging from 33,187,312 bp to 33,191,805 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g58250 | bZIP transcription factor domain containing protein, expressed; RAP ID: Os03g0796900; MSU ID: LOC_Os03g58250 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os03g58250 | Os03g0796900 | OsZIP33, RISBZ2, OsbZIP33 | rice endosperm bZIP, bZIP transcription factor 33, rice seed b-Zipper 2, b-ZIP transcription factor 33 | This gene encodes the rice transcription factor, REB (rice endosperm bZIP). D78609. | REB | ENDOSPERM BZIP |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0333189327 (J) | chr03 | 33189327 | CAAGG | CAAGC | 57.80% | 0.00% | CAAGC -> CAAGG | NA |
|
| STR0333189854 (J) | chr03 | 33189854 | CAAACAA | CAAACAG | 90.70% | 0.00% | CAAACAA -> CAAACAG | NA |
|
| STR0333189960 (J) | chr03 | 33189960 | G | A | 98.40% | 0.00% | G -> A | NA |
|
| vg0333187328 (J) | chr03 | 33187328 | GTAGTGA TATCTTT ATGCTTG GT | G | 57.60% | 0.19% | GTAGTGATAT CTTTATGCTT GGT -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g58250.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.128; most accessible tissue: Zhenshan97 young leaf, score: 92.594 |
| vg0333187371 (J) | chr03 | 33187371 | G | A | 54.00% | 0.30% | A -> G |
mr1181 (All); LR P-value: 1.37E-25;
mr1329 (All); LR P-value: 2.76E-12; mr1426 (All); LR P-value: 4.35E-28; mr1458 (All); LR P-value: 8.02E-43; mr1524 (All); LR P-value: 4.10E-11; mr1537 (All); LR P-value: 1.56E-24; mr1657 (All); LR P-value: 4.62E-12; mr1723 (All); LMM P-value: 6.69E-18; LR P-value: 6.80E-30; mr1723 (Ind_All); LMM P-value: 1.65E-17; LR P-value: 8.52E-22; mr1841 (All); LR P-value: 9.81E-24; mr1943 (All); LR P-value: 1.31E-22; mr1422_2 (All); LR P-value: 3.81E-23; mr1458_2 (All); LR P-value: 6.28E-48; mr1723_2 (All); LMM P-value: 1.29E-21; LR P-value: 1.18E-45; mr1723_2 (Ind_All); LMM P-value: 3.11E-22; LR P-value: 3.36E-29; mr1943_2 (All); LR P-value: 1.62E-25 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g58250.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.624; most accessible tissue: Zhenshan97 young leaf, score: 93.550 |
| vg0333187389 (J) | chr03 | 33187389 | A | G | 61.40% | 0.28% | G -> A |
mr1630 (All); LR P-value: 2.64E-10;
mr1645 (All); LR P-value: 9.89E-41; mr1647 (All); LR P-value: 9.98E-33; mr1682 (All); LR P-value: 3.35E-36; mr1723 (All); LMM P-value: 1.79E-16; LR P-value: 8.37E-47; mr1723 (Ind_All); LMM P-value: 6.42E-14; LR P-value: 1.76E-17; mr1754 (All); LR P-value: 1.11E-19; mr1723_2 (All); LMM P-value: 1.64E-15; LR P-value: 2.12E-51; mr1723_2 (Ind_All); LMM P-value: 1.62E-13; LR P-value: 3.27E-17 |
LOC_Os03g58250.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.878; most accessible tissue: Zhenshan97 young leaf, score: 93.846 |
| vg0333187556 (J) | chr03 | 33187556 | A | G | 99.50% | 0.00% | A -> G | NA |
LOC_Os03g58250.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.808; most accessible tissue: Zhenshan97 young leaf, score: 96.114 |
| vg0333187607 (J) | chr03 | 33187607 | GCATTAG CAATGTC TACGCCT GTC | G | 91.10% | 0.00% | GCATTAGCAA TGTCTACGCC TGTC -> G | NA |
LOC_Os03g58250.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.783; most accessible tissue: Zhenshan97 young leaf, score: 96.414 |
| vg0333187697 (J) | chr03 | 33187697 | G | A | 93.80% | 0.00% | G -> A | NA |
LOC_Os03g58250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.817; most accessible tissue: Zhenshan97 young leaf, score: 96.799 |
| vg0333187776 (J) | chr03 | 33187776 | G | T | 61.10% | 0.00% | T -> G |
LOC_Os03g58250.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 92.538; most accessible tissue: Zhenshan97 young leaf, score: 96.900 |
|
| vg0333187891 (J) | chr03 | 33187891 | G | A | 93.80% | 0.00% | G -> A | NA |
LOC_Os03g58250.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.654; most accessible tissue: Zhenshan97 young leaf, score: 96.653 |
| vg0333188005 (J) | chr03 | 33188005 | C | A | 93.80% | 0.00% | C -> A | NA |
LOC_Os03g58250.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.730; most accessible tissue: Zhenshan97 young leaf, score: 95.535 |
| vg0333188116 (J) | chr03 | 33188116 | G | T | 61.50% | 0.00% | T -> G |
mr1630 (All); LR P-value: 2.64E-10;
mr1645 (All); LR P-value: 9.89E-41; mr1647 (All); LR P-value: 9.98E-33; mr1682 (All); LR P-value: 3.35E-36; mr1723 (All); LMM P-value: 1.79E-16; LR P-value: 8.37E-47; mr1723 (Ind_All); LMM P-value: 6.42E-14; LR P-value: 1.76E-17; mr1754 (All); LR P-value: 1.11E-19; mr1723_2 (All); LMM P-value: 1.64E-15; LR P-value: 2.12E-51; mr1723_2 (Ind_All); LMM P-value: 1.62E-13; LR P-value: 3.27E-17 |
LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58250.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.696; most accessible tissue: Zhenshan97 young leaf, score: 94.037 |
| vg0333188403 (J) | chr03 | 33188403 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.352; most accessible tissue: Zhenshan97 young leaf, score: 87.004 |
| vg0333188432 (J) | chr03 | 33188432 | TTA | T | 99.80% | 0.00% | TTA -> T | NA |
LOC_Os03g58240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58250.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.583; most accessible tissue: Callus, score: 92.095 |
| vg0333188467 (J) | chr03 | 33188467 | C | G | 54.10% | 0.25% | G -> C |
mr1037 (All); LR P-value: 4.36E-26;
mr1169 (All); LR P-value: 8.25E-12; mr1181 (All); LR P-value: 6.94E-26; mr1329 (All); LR P-value: 1.11E-12; mr1426 (All); LR P-value: 3.83E-28; mr1457 (All); LR P-value: 1.51E-08; mr1458 (All); LR P-value: 2.17E-43; mr1524 (All); LR P-value: 2.78E-11; mr1537 (All); LR P-value: 1.38E-24; mr1657 (All); LR P-value: 3.84E-12; mr1723 (All); LMM P-value: 1.64E-16; LR P-value: 5.69E-29; mr1723 (Ind_All); LMM P-value: 1.65E-17; LR P-value: 8.52E-22; mr1841 (All); LR P-value: 1.00E-23; mr1943 (All); LR P-value: 1.43E-22; mr1164_2 (All); LR P-value: 9.68E-21; mr1244_2 (All); LR P-value: 4.49E-24; mr1458_2 (All); LR P-value: 2.49E-48; mr1723_2 (All); LMM P-value: 6.02E-21; LR P-value: 5.09E-45; mr1723_2 (Ind_All); LMM P-value: 3.11E-22; LR P-value: 3.36E-29; mr1943_2 (All); LR P-value: 3.96E-25 |
LOC_Os03g58250.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os03g58240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.427; most accessible tissue: Callus, score: 92.095 |
| vg0333188610 (J) | chr03 | 33188610 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os03g58240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g58250.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.392; most accessible tissue: Zhenshan97 young leaf, score: 83.199 |
| vg0333188886 (J) | chr03 | 33188886 | A | G | 61.20% | 0.23% | G -> A |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.112; most accessible tissue: Callus, score: 70.711 |
|
| vg0333189007 (J) | chr03 | 33189007 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g58260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g58250.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 57.519; most accessible tissue: Callus, score: 87.099 |
| vg0333189040 (J) | chr03 | 33189040 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g58260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 58.203; most accessible tissue: Callus, score: 87.099 |
| vg0333189116 (J) | chr03 | 33189116 | A | G | 61.20% | 0.00% | G -> A |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.038; most accessible tissue: Zhenshan97 young leaf, score: 76.099 |
|
| vg0333189200 (J) | chr03 | 33189200 | T | A | 57.30% | 0.36% | T -> A |
mr1441 (Ind_All); LR P-value: 5.74E-07;
mr1723 (All); LMM P-value: 3.78E-08; mr1723 (Ind_All); LMM P-value: 1.45E-07; LR P-value: 1.37E-09; mr1062_2 (Ind_All); LR P-value: 1.57E-07; mr1124_2 (Ind_All); LR P-value: 2.54E-08; mr1723_2 (All); LMM P-value: 5.12E-11; LR P-value: 2.24E-36; mr1723_2 (Ind_All); LMM P-value: 1.01E-09; LR P-value: 7.37E-13; mr1910_2 (All); LR P-value: 6.47E-06 |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.205; most accessible tissue: Callus, score: 86.532 |
| vg0333189303 (J) | chr03 | 33189303 | T | A | 99.30% | 0.00% | T -> A | NA |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g58260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.215; most accessible tissue: Callus, score: 86.532 |
| vg0333189331 (J) | chr03 | 33189331 | G | C | 54.20% | 0.02% | C -> G |
mr1037 (All); LR P-value: 4.36E-26;
mr1169 (All); LR P-value: 8.25E-12; mr1181 (All); LR P-value: 6.94E-26; mr1329 (All); LR P-value: 1.11E-12; mr1426 (All); LR P-value: 3.83E-28; mr1457 (All); LR P-value: 1.51E-08; mr1458 (All); LR P-value: 2.17E-43; mr1524 (All); LR P-value: 2.78E-11; mr1537 (All); LR P-value: 1.38E-24; mr1657 (All); LR P-value: 3.84E-12; mr1723 (All); LMM P-value: 1.64E-16; LR P-value: 5.69E-29; mr1723 (Ind_All); LMM P-value: 1.65E-17; LR P-value: 8.52E-22; mr1841 (All); LR P-value: 1.00E-23; mr1943 (All); LR P-value: 1.43E-22; mr1164_2 (All); LR P-value: 9.68E-21; mr1244_2 (All); LR P-value: 4.49E-24; mr1458_2 (All); LR P-value: 2.49E-48; mr1723_2 (All); LMM P-value: 6.02E-21; LR P-value: 5.09E-45; mr1723_2 (Ind_All); LMM P-value: 3.11E-22; LR P-value: 3.36E-29; mr1943_2 (All); LR P-value: 3.96E-25 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os03g58240.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58250.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.950; most accessible tissue: Zhenshan97 young leaf, score: 82.539 |
| vg0333189579 (J) | chr03 | 33189579 | A | AT | 61.40% | 0.28% | AT -> A | NA |
LOC_Os03g58240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g58260.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g58250.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 67.701; most accessible tissue: Zhenshan97 young leaf, score: 79.783 |
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