RiceVarMap2

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16 variations found. Os02g0752800/LOC_Os02g51670 (ethylene-responsive transcription factor; putative; expressed), ranging from 31,648,467 bp to 31,650,538 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene ID	Annotation
LOC_Os02g51670	ethylene-responsive transcription factor, putative, expressed; RAP ID: Os02g0752800; MSU ID: LOC_Os02g51670

MSU ID	RAP ID	Symbol	Name	Explanation	Recommended Gene Symbol	Recommended Gene Name
LOC_Os02g51670	Os02g0752800	OsERF#049, OsERF049, OsERF49, AP2/EREBP#132, AP2/EREBP132	ethylene response factor 49, APETALA2/ethylene-responsive element binding protein 132		ERF49	ETHYLENE RESPONSE FACTOR 49

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
STR0231648508 (J)	chr02	31648508	CATCCCA TCCCA	CATCCCA TCCCATC CCA	62.70%	0.00%	CATCCCATCC CATCCCA -> CATCCCATCC CA	NA
STR0231648550 (J)	chr02	31648550	AG	AA	62.80%	0.00%	AA -> AG	NA
STR0231650226 (J)	chr02	31650226	AGTAGTA GTAAGGT	AGTAGTA ATAAGGT	48.30%	0.00%	AGTAGTAGTA AGGT -> AGTAGTAATA AGGT	NA
vg0231648507 (J)	chr02	31648507	A	ACATCC	62.80%	0.00%	ACATCC -> A	NA	LOC_Os02g51670.1 Alt: A\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.109; most accessible tissue: Minghui63 flower, score: 99.835
vg0231648551 (J)	chr02	31648551	G	A	64.30%	0.00%	A -> G	NA	LOC_Os02g51670.1 Alt: G\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.134; most accessible tissue: Minghui63 flower, score: 99.858
vg0231648928 (J)	chr02	31648928	T	C	99.40%	0.00%	T -> C	NA	LOC_Os02g51670.1 Alt: C\| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.134; most accessible tissue: Minghui63 flag leaf, score: 99.075
vg0231649432 (J)	chr02	31649432	C	A	97.70%	0.00%	C -> A	NA	LOC_Os02g51670.1 Alt: A\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 96.403; most accessible tissue: Minghui63 flag leaf, score: 99.445
vg0231649597 (J)	chr02	31649597	C	T	98.50%	0.00%	C -> T	NA	LOC_Os02g51670.1 Alt: T\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.703; most accessible tissue: Minghui63 flag leaf, score: 99.457
vg0231649911 (J)	chr02	31649911	T	C	54.40%	0.00%	C -> T	mr1218 (All); LR P-value: 1.10E-14; mr1218_2 (All); LR P-value: 3.12E-19; mr1781_2 (All); LR P-value: 3.47E-11	LOC_Os02g51670.1 Alt: T\| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 94.316; most accessible tissue: Minghui63 flag leaf, score: 99.337
vg0231650032 (J)	chr02	31650032	C	T	89.30%	0.00%	C -> T	mr1564 (All); LR P-value: 2.17E-06; mr1717_2 (Ind_All); LR P-value: 6.97E-06; mr1722_2 (Ind_All); LR P-value: 5.15E-06; mr1910_2 (Ind_All); LR P-value: 4.41E-06	LOC_Os02g51670.1 Alt: T\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 97.761; most accessible tissue: Minghui63 flag leaf, score: 99.331
vg0231650071 (J)	chr02	31650071	G	C	92.70%	0.00%	G -> C	NA	LOC_Os02g51670.1 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.652; most accessible tissue: Minghui63 flag leaf, score: 99.237
vg0231650106 (J)	chr02	31650106	C	T	99.80%	0.00%	C -> T	NA	LOC_Os02g51670.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.269; most accessible tissue: Minghui63 flag leaf, score: 99.194
vg0231650122 (J)	chr02	31650122	C	T	95.10%	0.00%	C -> T	mr1114 (Jap_All); LR P-value: 9.87E-06; mr1117 (Jap_All); LR P-value: 5.20E-07; mr1118 (Jap_All); LR P-value: 3.65E-08; mr1119 (Jap_All); LR P-value: 1.16E-06; mr1123 (Jap_All); LR P-value: 8.61E-07; mr1242 (Jap_All); LR P-value: 3.52E-07; mr1495 (Jap_All); LR P-value: 5.85E-06; mr1496 (Jap_All); LR P-value: 2.53E-07; mr1113_2 (Jap_All); LMM P-value: 1.85E-07; LR P-value: 1.04E-10; mr1114_2 (Jap_All); LR P-value: 1.89E-07; mr1117_2 (Jap_All); LR P-value: 6.67E-09; mr1118_2 (Jap_All); LR P-value: 1.75E-09; mr1119_2 (Jap_All); LR P-value: 9.11E-09; mr1120_2 (Jap_All); LR P-value: 2.14E-07; mr1123_2 (Jap_All); LR P-value: 3.95E-08; mr1183_2 (Jap_All); LR P-value: 1.71E-06; mr1240_2 (Jap_All); LR P-value: 1.07E-09; mr1242_2 (Jap_All); LR P-value: 2.76E-08; mr1247_2 (Jap_All); LR P-value: 3.18E-07; mr1495_2 (Jap_All); LR P-value: 1.31E-08; mr1496_2 (Jap_All); LR P-value: 5.19E-11; mr1936_2 (Jap_All); LR P-value: 7.91E-06	LOC_Os02g51670.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.062; most accessible tissue: Minghui63 flag leaf, score: 99.114
vg0231650199 (J)	chr02	31650199	G	A	89.30%	0.00%	G -> A	mr1564 (All); LR P-value: 3.82E-06; mr1717_2 (Ind_All); LR P-value: 6.32E-06; mr1722_2 (Ind_All); LR P-value: 4.39E-06; mr1910_2 (Ind_All); LR P-value: 3.94E-06	LOC_Os02g51670.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.847; most accessible tissue: Minghui63 flag leaf, score: 99.132
vg0231650233 (J)	chr02	31650233	G	A	56.40%	0.00%	G -> A	Grain_thickness (Ind_All); LR P-value: 1.74E-09; mr1598 (All); LR P-value: 2.23E-19; mr1712 (All); LR P-value: 1.42E-10; mr1717 (All); LR P-value: 1.17E-08; mr1770 (All); LR P-value: 1.20E-09; mr1946 (All); LR P-value: 5.33E-09; mr1123_2 (Ind_All); LR P-value: 8.53E-07; mr1272_2 (All); LR P-value: 7.71E-07; mr1478_2 (All); LR P-value: 1.54E-08; mr1531_2 (All); LR P-value: 2.32E-22; mr1717_2 (All); LR P-value: 1.38E-12; mr1722_2 (Ind_All); LMM P-value: 2.03E-06; LR P-value: 8.12E-09; mr1728_2 (All); LR P-value: 2.00E-13; mr1835_2 (All); LR P-value: 6.99E-09; mr1860_2 (All); LR P-value: 1.27E-08; mr1904_2 (All); LR P-value: 1.42E-12; mr1904_2 (Ind_All); LR P-value: 2.54E-07; mr1910_2 (All); LR P-value: 3.63E-07; mr1936_2 (Ind_All); LR P-value: 4.58E-07; mr1946_2 (All); LR P-value: 6.67E-09; mr1948_2 (All); LR P-value: 6.67E-09	LOC_Os02g51670.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.964; most accessible tissue: Minghui63 flag leaf, score: 99.196
vg0231650424 (J)	chr02	31650424	TATG	T	64.30%	0.02%	T -> TATG	NA	LOC_Os02g51670.1 Alt: TATG\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.528; most accessible tissue: Minghui63 flag leaf, score: 99.440

Showing 1 to 16 of 16 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:

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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