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Search Results:

3 variations found. Os07g0624900/LOC_Os07g43180 (SKP1-like protein 1B; putative; expressed), ranging from 25,884,417 bp to 25,885,020 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os07g43180 SKP1-like protein 1B, putative; RAP ID: Os07g0624900; MSU ID: LOC_Os07g43180

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:

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
vg0725884651 (J) chr07 25884651 C T 62.30% 0.00% T -> C
mr1070 (All); LR P-value: 1.99E-10;
mr1386 (All); LR P-value: 1.02E-12;
mr1414 (All); LR P-value: 7.55E-27;
mr1039_2 (All); LR P-value: 8.31E-28;
mr1128_2 (All); LR P-value: 1.01E-13;
mr1304_2 (All); LMM P-value: 8.67E-06; LR P-value: 1.80E-24;
mr1632_2 (All); LR P-value: 1.36E-33;
mr1873_2 (All); LR P-value: 1.76E-32
LOC_Os07g43180.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.472; most accessible tissue: Zhenshan97 young leaf, score: 92.035
vg0725884656 (J) chr07 25884656 C CCGGCGG CGG 59.60% 0.00% CCGGCGGCGG -> C NA
LOC_Os07g43180.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 87.351; most accessible tissue: Zhenshan97 young leaf, score: 91.967
STR0725884657 (J) chr07 25884657 C CGGCGGC GGC 58.90% 0.00% CGGCGGCGGC -> C NA