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Search Results:

2 variations found. Os11g0117400/LOC_Os11g02520 (WRKY104; expressed), ranging from 782,357 bp to 783,511 bp (including 0 kb upstream and 0 kb downstream of the gene).

MSU IDRAP IDSymbolNameExplanationRecommended Gene SymbolRecommended Gene Name
LOC_Os11g02520Os11g0117400OsWRKY104WRKY9 in Zhang and Wang (2005) and in Berri et al. (2009). WRKY89 in Wu et al. (2005). WRKY100 in Ross et al.(2007).WRKY104WRKY GENE 104

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

The 'big effect' variations are marked out:

ColorExplainDetails
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:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg1100782434 (J) chr11 782434 T A 99.70% 0.00% T -> A NA
LOC_Os11g02520.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os11g02500.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g02510.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 40.020; most accessible tissue: Minghui63 young leaf, score: 58.210
vg1100783127 (J) chr11 783127 A C 99.90% 0.00% A -> C NA
LOC_Os11g02510.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g02530.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os11g02520.1 Alt: C| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 58.986; most accessible tissue: Minghui63 young leaf, score: 83.907