Nucleotide sequence alignment and predicted protein structure depicting the functional relevance of non-synonymous SNP in abiotic stress-responsive WRKY gene. Non-synonymous SNP validated in WRKY family (OsWRKY35V2) transcription factor gene (LOC_Os04g39570) showing differentiation between 22 drought tolerant upland indica/aus and 30 drought sensitive lowland rice genotype groups. Missense transversional substitution of the second nucleotide in the triplet codon of upland indica/aus genotypes coding for amino acid in the conserved DNA binding domain of WRKY by another nucleotide resulted in the formation of new triplet codon encoding for novel amino acid in lowland indica group. The substitution mutation was predicted to alter three dimensional secondary structure of protein including the DNA binding domain in WRKY which may produce functionally different protein between upland and lowland genotypes. Missense non-synonymous SNP site, different protein structure and DNA binding domain are highlighted.