11 variations found. Os04g0587400/LOC_Os04g49748 (purine permease; putative; expressed), ranging from 29,660,958 bp to 29,662,569 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g49748 | purine permease, putative, expressed; RAP ID: Os04g0587400; MSU ID: LOC_Os04g49748 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os04g49748 | Os04g0587400 | OsPUP6 | purine permease 6, PUP-type cytokinin transporter 6 | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0429660993 (J) | chr04 | 29660993 | T | C | 97.40% | 0.00% | T -> C | NA |
LOC_Os04g49748.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49739.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.097; most accessible tissue: Zhenshan97 young leaf, score: 97.427 |
| vg0429661205 (J) | chr04 | 29661205 | G | T | 73.30% | 0.00% | G -> T |
LOC_Os04g49757.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49739.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49748.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.972; most accessible tissue: Zhenshan97 flag leaf, score: 97.492 |
|
| vg0429661279 (J) | chr04 | 29661279 | TGCGGCG GCGGCGG CGGCGGC GGCGCCG CTGCCGC CTGTGTC CAGCCAG CGGCTGC GGTGGTG G | TGCGGCG GCGGCGC CGCTGCC GCCTGTG TCCAGCC AGCGGCT GCGGTGG TGG | 98.90% | 0.00% | TGCGGCGGCG GCGGCGGCGG CGGCGCCGCT GCCGCCTGTG TCCAGCCAGC GGCTGCGGTG GTGG -> TGCGGCGGCG GCGCCGCTGC CGCCTGTGTC CAGCCAGCGG CTGCGGTGGT GG,T,TGCGG CGGCGGCGGC GGCGGCGGCG GCGCCGCTGC CGCCTGTGTC CAGCCAGCGG CTGCGGTGGT GG,TGCGGCG GCGGCGGCGG CGGCGGCGGC GGCGGCGGCG GCGCCGCTGC CGCCTGTGTC CAGCCAGCGG CTGCGGTGGT GG,TGCGGCG GCGGCGGCGG CGGCGGCGGC GGCGGCGGCG CCGCTGCCGC CTGTGTCCAG CCAGCGGCTG CGGTGGTGG | NA |
LOC_Os04g49748.1 Alt: TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os04g49748.1 Alt: TGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os04g49748.1 Alt: TGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os04g49748.1 Alt: TGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCCGCTGCCGCCTGTGTCCAGCCAGCGGCTGCGGTGGTGG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os04g49748.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 92.748; most accessible tissue: Zhenshan97 flag leaf, score: 97.876 |
| vg0429661444 (J) | chr04 | 29661444 | T | G | 55.90% | 0.00% | G -> T | NA |
LOC_Os04g49748.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.706; most accessible tissue: Zhenshan97 flag leaf, score: 98.062 |
| vg0429661448 (J) | chr04 | 29661448 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os04g49748.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os04g49757.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g49730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g49739.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.688; most accessible tissue: Zhenshan97 flag leaf, score: 98.069 |
| vg0429661627 (J) | chr04 | 29661627 | T | G | 52.50% | 0.19% | G -> T |
mr1076 (All); LR P-value: 5.21E-26;
mr1083 (All); LR P-value: 3.03E-22; mr1169 (All); LR P-value: 1.06E-12; mr1195 (All); LR P-value: 2.25E-10; mr1200 (All); LR P-value: 1.14E-41; mr1264 (All); LR P-value: 8.31E-24; mr1281 (All); LR P-value: 1.08E-11; mr1426 (All); LR P-value: 6.35E-29; mr1509 (All); LR P-value: 1.05E-42; mr1519 (All); LR P-value: 4.14E-46; mr1526 (All); LR P-value: 1.55E-43; mr1531 (All); LR P-value: 4.42E-13; mr1558 (All); LR P-value: 4.54E-47; mr1560 (All); LR P-value: 1.16E-30; mr1571 (All); LR P-value: 7.62E-25; mr1581 (All); LR P-value: 6.06E-10; mr1655 (All); LR P-value: 7.35E-14; mr1671 (All); LR P-value: 6.93E-61; mr1745 (All); LR P-value: 1.06E-30; mr1793 (All); LR P-value: 5.23E-31; mr1798 (All); LR P-value: 2.24E-49; mr1819 (All); LR P-value: 1.32E-10; mr1841 (All); LR P-value: 4.81E-23; mr1883 (All); LR P-value: 3.13E-12; mr1943 (All); LR P-value: 4.61E-21; mr1970 (All); LR P-value: 2.57E-65; mr1973 (All); LR P-value: 9.13E-84; mr1509_2 (All); LR P-value: 9.88E-45; mr1531_2 (All); LR P-value: 1.27E-18; mr1571_2 (All); LR P-value: 6.80E-35; mr1721_2 (All); LR P-value: 5.77E-48; mr1793_2 (All); LR P-value: 6.24E-46; mr1798_2 (All); LR P-value: 8.68E-71; mr1970_2 (All); LR P-value: 1.33E-61; mr1973_2 (All); LR P-value: 2.52E-95 |
LOC_Os04g49748.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g49748.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 90.958; most accessible tissue: Zhenshan97 flag leaf, score: 97.991 |
| vg0429661861 (J) | chr04 | 29661861 | G | C | 53.20% | 0.34% | C -> G |
mr1037 (All); LR P-value: 4.04E-26;
mr1076 (All); LR P-value: 8.75E-26; mr1083 (All); LR P-value: 2.20E-22; mr1169 (All); LR P-value: 7.43E-13; mr1195 (All); LR P-value: 2.63E-10; mr1281 (All); LR P-value: 4.75E-12; mr1342 (All); LR P-value: 1.43E-08; mr1426 (All); LR P-value: 6.74E-28; mr1437 (All); LR P-value: 1.00E-39; mr1509 (All); LR P-value: 9.45E-42; mr1519 (All); LR P-value: 2.90E-47; mr1526 (All); LR P-value: 8.01E-42; mr1560 (All); LR P-value: 1.15E-29; mr1571 (All); LR P-value: 3.00E-23; mr1655 (All); LR P-value: 4.72E-13; mr1671 (All); LR P-value: 1.33E-57; mr1717 (All); LR P-value: 7.82E-07; mr1793 (All); LR P-value: 1.74E-29; mr1819 (All); LR P-value: 1.53E-10; mr1940 (All); LR P-value: 2.47E-12; mr1970 (All); LR P-value: 1.40E-63; mr1973 (All); LR P-value: 1.69E-82; mr1164_2 (All); LR P-value: 2.49E-21; mr1509_2 (All); LR P-value: 3.66E-45; mr1558_2 (All); LR P-value: 3.92E-57; mr1571_2 (All); LR P-value: 4.04E-35; mr1793_2 (All); LR P-value: 1.26E-46; mr1798_2 (All); LR P-value: 6.99E-69; mr1922_2 (All); LR P-value: 6.23E-20; mr1940_2 (All); LR P-value: 2.48E-08; mr1970_2 (All); LR P-value: 1.37E-62; mr1973_2 (All); LR P-value: 1.01E-95 |
LOC_Os04g49748.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g49748.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.528; most accessible tissue: Zhenshan97 flag leaf, score: 97.225 |
| vg0429661960 (J) | chr04 | 29661960 | T | G | 53.30% | 0.34% | G -> T |
mr1037 (All); LR P-value: 2.04E-26;
mr1076 (All); LR P-value: 1.82E-26; mr1083 (All); LR P-value: 8.69E-23; mr1169 (All); LR P-value: 4.38E-13; mr1195 (All); LR P-value: 2.80E-10; mr1246 (All); LR P-value: 1.35E-60; mr1264 (All); LR P-value: 6.99E-24; mr1281 (All); LR P-value: 5.52E-12; mr1342 (All); LR P-value: 9.25E-09; mr1416 (All); LR P-value: 1.96E-21; mr1426 (All); LR P-value: 4.55E-28; mr1437 (All); LR P-value: 6.13E-40; mr1509 (All); LR P-value: 2.30E-42; mr1519 (All); LR P-value: 4.71E-48; mr1526 (All); LR P-value: 9.42E-43; mr1558 (All); LR P-value: 2.17E-46; mr1560 (All); LR P-value: 3.23E-30; mr1571 (All); LR P-value: 8.86E-24; mr1655 (All); LR P-value: 3.44E-13; mr1671 (All); LR P-value: 4.54E-59; mr1793 (All); LR P-value: 3.83E-30; mr1798 (All); LR P-value: 7.33E-49; mr1819 (All); LR P-value: 2.50E-10; mr1878 (All); LR P-value: 3.13E-31; mr1883 (All); LR P-value: 2.23E-11; mr1940 (All); LR P-value: 1.33E-12; mr1943 (All); LR P-value: 5.80E-21; mr1970 (All); LR P-value: 1.07E-63; mr1973 (All); LR P-value: 8.53E-82; mr1164_2 (All); LR P-value: 1.04E-20; mr1509_2 (All); LR P-value: 3.87E-45; mr1558_2 (All); LR P-value: 1.33E-56; mr1571_2 (All); LR P-value: 1.08E-34; mr1793_2 (All); LR P-value: 2.16E-46; mr1798_2 (All); LR P-value: 1.55E-70; mr1922_2 (All); LR P-value: 3.00E-19; mr1970_2 (All); LR P-value: 3.03E-62; mr1973_2 (All); LR P-value: 5.76E-95 |
LOC_Os04g49748.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g49748.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.435; most accessible tissue: Zhenshan97 flag leaf, score: 97.465 |
| vg0429661993 (J) | chr04 | 29661993 | A | C | 55.90% | 0.34% | C -> A | NA |
LOC_Os04g49748.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g49748.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 94.353; most accessible tissue: Zhenshan97 flag leaf, score: 97.361 |
| vg0429662407 (J) | chr04 | 29662407 | CT | CTT | 64.10% | 0.00% | C -> CT,CTT,CTT T | NA |
LOC_Os04g49748.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49757.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49739.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49748.1 Alt: CTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49757.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49739.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49748.1 Alt: CTTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49757.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49739.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.523; most accessible tissue: Minghui63 young leaf, score: 98.089 |
| STR0429662408 (J) | chr04 | 29662408 | TT | TTTT | 69.10% | 0.00% | T -> TT,TTT,TTT T | NA |
|