RiceVarMap2

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21 variations found. Os04g0394500/LOC_Os04g32350 (RNA polymerase III RPC4 domain containing protein; expressed), ranging from 19,398,844 bp to 19,401,436 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene ID	Annotation
LOC_Os04g32350	RNA polymerase III RPC4 domain containing protein, expressed; RAP ID: Os04g0394500; MSU ID: LOC_Os04g32350

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

Category	Variant ID	Chrom	Pos	Gene	MSU	RAP	Alt_Allele_Function	Ref_geno	Alt_geno
Yield components	vg0419403332	Chr4	19403332	DGS1/RPC4	LOC_Os04g32350	Os04g0394500	hybrid incompatibility	T	C

Gene Expression Atlas:

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.

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

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.

Detailed Variation Information:

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Var ID	Chrom	Position	Primary Allele	Secondary Allele	Primary Allele Frequency	DEL Frequency	Var	GWAS Results	Effect
vg0419398950 (J)	chr04	19398950	G	Unkown	99.70%	0.00%	G -> A	NA	LOC_Os04g32350.1 Alt: A\| synonymous_variant LOW(snpEff) The average chromatin accessibility score: 98.920; most accessible tissue: Minghui63 flag leaf, score: 99.965
vg0419399067 (J)	chr04	19399067	C	Unkown	77.30%	12.91%	C -> G	NA	LOC_Os04g32350.1 Alt: G\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 99.014; most accessible tissue: Minghui63 flag leaf, score: 99.970
vg0419399338 (J)	chr04	19399338	G	Unkown	87.70%	8.63%	G -> A	NA	The average chromatin accessibility score: 98.263; most accessible tissue: Minghui63 flag leaf, score: 99.968
vg0419399394 (J)	chr04	19399394	T	A	99.80%	0.00%	T -> A	NA	LOC_Os04g32350.1 Alt: A\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.249; most accessible tissue: Minghui63 flag leaf, score: 99.969
vg0419399468 (J)	chr04	19399468	G	Unkown	87.80%	6.96%	G -> T	NA	LOC_Os04g32350.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.758; most accessible tissue: Minghui63 flag leaf, score: 99.958
vg0419399577 (J)	chr04	19399577	G	A	99.40%	0.00%	G -> A	NA	LOC_Os04g32350.1 Alt: A\| synonymous_variant LOW(snpEff) The average chromatin accessibility score: 97.916; most accessible tissue: Minghui63 flag leaf, score: 99.968
vg0419399639 (J)	chr04	19399639	C	T	97.60%	1.95%	C -> T	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.887; most accessible tissue: Minghui63 flag leaf, score: 99.968
vg0419399747 (J)	chr04	19399747	T	Unkown	46.40%	51.08%	T -> C	NA	LOC_Os04g32350.1 Alt: C\| missense_variant MODERATE(snpEff) The average chromatin accessibility score: 98.417; most accessible tissue: Minghui63 flag leaf, score: 99.957
vg0419400199 (J)	chr04	19400199	A	Unkown	41.50%	53.77%	A -> T	NA	LOC_Os04g32350.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.882; most accessible tissue: Minghui63 flag leaf, score: 99.950
vg0419400230 (J)	chr04	19400230	C	Unkown	62.70%	30.24%	C -> T	NA	LOC_Os04g32350.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.804; most accessible tissue: Minghui63 flag leaf, score: 99.941
vg0419400406 (J)	chr04	19400406	C	Unkown	96.60%	0.97%	C -> T	NA	LOC_Os04g32350.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.004; most accessible tissue: Minghui63 flag leaf, score: 99.936
vg0419400533 (J)	chr04	19400533	C	Unkown	54.60%	42.64%	C -> G	NA	LOC_Os04g32350.1 Alt: G\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.681; most accessible tissue: Minghui63 flag leaf, score: 99.945
vg0419400563 (J)	chr04	19400563	C	Unkown	53.50%	43.97%	C -> G,T	NA	LOC_Os04g32350.1 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os04g32350.1 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.622; most accessible tissue: Minghui63 flag leaf, score: 99.938
vg0419400569 (J)	chr04	19400569	GAA	GAAA	32.70%	55.82%	GAA -> G,GA,GAAA	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: GAAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os04g32350.1 Alt: GA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.602; most accessible tissue: Minghui63 flag leaf, score: 99.936
vg0419400709 (J)	chr04	19400709	T	C	45.60%	53.09%	T -> C	NA	LOC_Os04g32350.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.000; most accessible tissue: Minghui63 flag leaf, score: 99.938
vg0419400894 (J)	chr04	19400894	G	Unkown	88.30%	10.83%	G -> A	NA	LOC_Os04g32350.1 Alt: A\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.223; most accessible tissue: Minghui63 flag leaf, score: 99.931
vg0419400928 (J)	chr04	19400928	G	Unkown	87.30%	11.93%	G -> A	NA	LOC_Os04g32350.1 Alt: A\| missense_variant MODERATE(snpEff) The average chromatin accessibility score: 96.568; most accessible tissue: Minghui63 flag leaf, score: 99.917
vg0419401156 (J)	chr04	19401156	ACT	ACTCT	44.20%	51.27%	ACT -> A,ACTCT	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: ACTCT\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.190; most accessible tissue: Minghui63 flag leaf, score: 99.917
vg0419401336 (J)	chr04	19401336	G	GA	69.20%	19.23%	GA -> G,GAA	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: GAA\| intron_variant MODIFIER(snpEff) LOC_Os04g32350.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.487; most accessible tissue: Minghui63 flag leaf, score: 99.928
vg0419401408 (J)	chr04	19401408	T	Unkown	99.50%	0.51%	T -> A	NA	LOC_Os04g32350.1 Alt: A\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.479; most accessible tissue: Minghui63 flag leaf, score: 99.926
vg0419401413 (J)	chr04	19401413	C	CA	86.30%	13.10%	C -> A,CA	NA	LOC_Os04g32350.1 Alt: CA\| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: A\| splice_region_variant&intron_variant LOW(snpEff) The average chromatin accessibility score: 94.485; most accessible tissue: Minghui63 flag leaf, score: 99.927

Showing 1 to 21 of 21 entries

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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

QTN in RiceNavi

Gene Expression Atlas:

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

Detailed Variation Information:

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