23 variations found. Os03g0148700/LOC_Os03g05470 (tyrosine protein kinase domain containing protein; putative; expressed), ranging from 2,707,462 bp to 2,710,821 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g05470 | tyrosine protein kinase domain containing protein, putative, expressed; RAP ID: Os03g0148700; MSU ID: LOC_Os03g05470 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0302707462 (J) | chr03 | 2707462 | C | T | 97.20% | 0.00% | C -> T | NA |
LOC_Os03g05470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05460-LOC_Os03g05470 Alt: T| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.951; most accessible tissue: Callus, score: 99.017 |
| vg0302707497 (J) | chr03 | 2707497 | G | T | 65.20% | 0.00% | T -> G | NA |
LOC_Os03g05470.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.221; most accessible tissue: Callus, score: 99.017 |
| vg0302707532 (J) | chr03 | 2707532 | C | A | 65.40% | 0.00% | A -> C | NA |
LOC_Os03g05470.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.362; most accessible tissue: Callus, score: 99.017 |
| vg0302707572 (J) | chr03 | 2707572 | AGG | A | 64.70% | 0.00% | A -> AGG,G | NA |
LOC_Os03g05470.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05470.1 Alt: AGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.464; most accessible tissue: Callus, score: 99.017 |
| vg0302707602 (J) | chr03 | 2707602 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g05470.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 91.878; most accessible tissue: Zhenshan97 flag leaf, score: 97.673 |
| vg0302707604 (J) | chr03 | 2707604 | G | A | 97.00% | 0.00% | G -> A | NA |
LOC_Os03g05470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.885; most accessible tissue: Zhenshan97 flag leaf, score: 97.678 |
| vg0302707918 (J) | chr03 | 2707918 | G | GT | 99.60% | 0.00% | G -> GT | NA |
The average chromatin accessibility score: 84.425; most accessible tissue: Zhenshan97 flag leaf, score: 94.613
|
| vg0302708026 (J) | chr03 | 2708026 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os03g05470.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 81.670; most accessible tissue: Minghui63 root, score: 94.901 |
| vg0302708146 (J) | chr03 | 2708146 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os03g05470.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 81.687; most accessible tissue: Minghui63 root, score: 97.067 |
| vg0302708193 (J) | chr03 | 2708193 | C | CA | 99.90% | 0.00% | C -> CA | NA |
The average chromatin accessibility score: 81.125; most accessible tissue: Callus, score: 97.544
|
| vg0302708232 (J) | chr03 | 2708232 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os03g05470.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 77.873; most accessible tissue: Callus, score: 97.544 |
| vg0302708290 (J) | chr03 | 2708290 | G | A | 65.00% | 0.00% | A -> G | NA |
LOC_Os03g05470.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.340; most accessible tissue: Callus, score: 97.544 |
| vg0302708574 (J) | chr03 | 2708574 | T | TATTAAT TA | 41.20% | 0.00% | T -> TATTAATTA, TATTAATTAA TTAATTA,TA TTA,TATTAA TTAATTA,TA TTATTTA,TA TTAATTAATT AATTAATTA | NA |
LOC_Os03g05480.1 Alt: TATTAATTAATTAATTAATTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05470.1 Alt: TATTAATTAATTAATTAATTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05480.1 Alt: TATTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05470.1 Alt: TATTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05480.1 Alt: TATTAATTAATTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05470.1 Alt: TATTAATTAATTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05480.1 Alt: TATTAATTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05470.1 Alt: TATTAATTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05480.1 Alt: TATTAATTAATTAATTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05470.1 Alt: TATTAATTAATTAATTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05480.1 Alt: TATTATTTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g05470.1 Alt: TATTATTTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.568; most accessible tissue: Callus, score: 97.086 |
| vg0302708596 (J) | chr03 | 2708596 | T | TTAATTA | 99.70% | 0.00% | T -> TTAATTA,TT A | NA |
LOC_Os03g05480.1 Alt: TTA| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g05470.1 Alt: TTA| intron_variant MODIFIER(snpEff) LOC_Os03g05480.1 Alt: TTAATTA| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g05470.1 Alt: TTAATTA| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.499; most accessible tissue: Minghui63 root, score: 89.190 |
| vg0302708845 (J) | chr03 | 2708845 | A | C | 64.70% | 0.00% | C -> A | NA |
LOC_Os03g05470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.451; most accessible tissue: Minghui63 young leaf, score: 81.500 |
| vg0302709030 (J) | chr03 | 2709030 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os03g05480.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g05470.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.169; most accessible tissue: Callus, score: 85.954 |
| vg0302709042 (J) | chr03 | 2709042 | T | G | 99.50% | 0.00% | T -> G | NA |
LOC_Os03g05480.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05470.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.356; most accessible tissue: Callus, score: 85.954 |
| vg0302709043 (J) | chr03 | 2709043 | T | C | 99.50% | 0.00% | T -> C | NA |
LOC_Os03g05480.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05470.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.060; most accessible tissue: Callus, score: 85.954 |
| vg0302709667 (J) | chr03 | 2709667 | T | A | 64.40% | 0.11% | A -> T | NA |
LOC_Os03g05480.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05470.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.890; most accessible tissue: Callus, score: 80.443 |
| vg0302709863 (J) | chr03 | 2709863 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os03g05470.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os03g05480.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.494; most accessible tissue: Zhenshan97 flag leaf, score: 81.985 |
| vg0302710212 (J) | chr03 | 2710212 | T | C | 65.50% | 0.02% | C -> T | NA |
LOC_Os03g05480.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05470.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.689; most accessible tissue: Callus, score: 90.930 |
| vg0302710387 (J) | chr03 | 2710387 | G | A | 65.40% | 0.00% | A -> G | NA |
LOC_Os03g05470.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.697; most accessible tissue: Minghui63 young leaf, score: 91.128 |
| vg0302710780 (J) | chr03 | 2710780 | A | G | 92.40% | 0.00% | A -> G | NA |
LOC_Os03g05470.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g05480.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.409; most accessible tissue: Minghui63 young leaf, score: 93.844 |