15 variations found. Os07g0568700/LOC_Os07g38130 (polygalacturonase inhibitor 1 precursor; putative; expressed), ranging from 22,874,251 bp to 22,875,707 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g38130 | polygalacturonase inhibitor 1 precursor, putative, expressed; RAP ID: Os07g0568700; MSU ID: LOC_Os07g38130 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os07g38130 | Os07g0568700 | OsFOR1, Osfor1 | rice floral organ regulator-1, Floral organ regulator 1 | Q8GT95. PO:0004706; flower primordium ; PO:0006318; floret (sensu Poaceae) ; PO:0005052; callus. GRO:0007158; spikelet development ; GRO:0007157; panicle development. AF466357. AAO17320. Polygalacturonase-inhibiting protein, PGIP protein | FOR1 | FLORAL ORGAN REGULATOR 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0722874347 (J) | chr07 | 22874347 | G | GCAT | 53.40% | 0.06% | G -> GCAT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g38130.1 Alt: GCAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g38140.1 Alt: GCAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.831; most accessible tissue: Minghui63 panicle, score: 99.892 |
| vg0722874398 (J) | chr07 | 22874398 | A | G | 96.10% | 0.00% | A -> G |
Awn_length (Jap_All); LR P-value: 7.13E-13;
mr1201 (Jap_All); LR P-value: 7.56E-06; mr1274 (Jap_All); LR P-value: 1.97E-06; mr1624 (Jap_All); LR P-value: 8.44E-09; mr1057_2 (Jap_All); LR P-value: 5.91E-08; mr1624_2 (Jap_All); LR P-value: 2.43E-09; mr1733_2 (Jap_All); LR P-value: 2.50E-07; mr1842_2 (Jap_All); LR P-value: 8.73E-06 |
LOC_Os07g38130.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.381; most accessible tissue: Minghui63 panicle, score: 99.876 |
| vg0722874413 (J) | chr07 | 22874413 | T | C | 91.40% | 0.00% | T -> C |
LOC_Os07g38130.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.149; most accessible tissue: Minghui63 panicle, score: 99.866 |
|
| vg0722874415 (J) | chr07 | 22874415 | C | T | 96.60% | 0.00% | C -> T |
LOC_Os07g38130.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.171; most accessible tissue: Minghui63 panicle, score: 99.867 |
|
| vg0722874422 (J) | chr07 | 22874422 | T | A | 99.00% | 0.00% | T -> A | NA |
LOC_Os07g38130.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.299; most accessible tissue: Minghui63 panicle, score: 99.873 |
| vg0722874459 (J) | chr07 | 22874459 | C | CT | 94.70% | 0.00% | C -> CT | NA |
LOC_Os07g38130.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.020; most accessible tissue: Minghui63 panicle, score: 99.871 |
| vg0722874621 (J) | chr07 | 22874621 | T | C | 59.90% | 0.15% | C -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g38130.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g38140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.064; most accessible tissue: Minghui63 panicle, score: 99.857 |
|
| vg0722874801 (J) | chr07 | 22874801 | G | A | 86.40% | 0.00% | G -> A |
mr1304 (Ind_All); LR P-value: 1.88E-06;
mr1343 (All); LR P-value: 6.79E-07; mr1376 (Ind_All); LR P-value: 2.26E-06; mr1431 (Ind_All); LR P-value: 2.26E-06; mr1530 (All); LR P-value: 4.64E-07; mr1820 (Ind_All); LR P-value: 6.50E-06; mr1830 (Ind_All); LR P-value: 9.48E-06; mr1388_2 (All); LR P-value: 4.81E-09 |
LOC_Os07g38130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.073; most accessible tissue: Minghui63 panicle, score: 99.618 |
| vg0722874861 (J) | chr07 | 22874861 | C | T | 58.80% | 0.32% | C -> T |
LOC_Os07g38130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g38130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.861; most accessible tissue: Minghui63 panicle, score: 99.482 |
|
| vg0722874941 (J) | chr07 | 22874941 | C | T | 94.10% | 0.00% | C -> T,G |
LOC_Os07g38130.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os07g38140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g38130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.845; most accessible tissue: Minghui63 panicle, score: 99.298 |
|
| vg0722875224 (J) | chr07 | 22875224 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os07g38130.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.015; most accessible tissue: Minghui63 panicle, score: 99.212 |
| vg0722875383 (J) | chr07 | 22875383 | C | T | 92.90% | 0.00% | C -> T,G | NA |
LOC_Os07g38130.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os07g38140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g38130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.552; most accessible tissue: Minghui63 panicle, score: 99.462 |
| vg0722875674 (J) | chr07 | 22875674 | G | A | 96.10% | 0.00% | G -> A |
Awn_length (Jap_All); LR P-value: 7.13E-13;
mr1201 (Jap_All); LR P-value: 7.56E-06; mr1274 (Jap_All); LR P-value: 1.97E-06; mr1624 (Jap_All); LR P-value: 8.44E-09; mr1057_2 (Jap_All); LR P-value: 5.91E-08; mr1624_2 (Jap_All); LR P-value: 2.43E-09; mr1733_2 (Jap_All); LR P-value: 2.50E-07; mr1842_2 (Jap_All); LR P-value: 8.73E-06 |
LOC_Os07g38130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g38150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.580; most accessible tissue: Minghui63 panicle, score: 99.888 |
| vg0722875693 (J) | chr07 | 22875693 | T | A | 94.10% | 0.00% | T -> A |
LOC_Os07g38130.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g38140.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g38150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.393; most accessible tissue: Minghui63 panicle, score: 99.911 |
|
| STR0722874348 (J) | chr07 | 22874348 | CATCATC | CATC | 47.30% | 0.00% | CATC -> CATCATC | NA |
|