MKRN gene family encodes zinc ring finger proteins characterized by a unique array of motifs (C3H, RING and a characteristic cys-his motif) in eukaryotes. To elucidate the function of the MKRN gene and to draw an analogy between plant root apical meristem and animal brain, we compared the gene expression pattern of MKRN in plant seeds with that of mouse embryo. The spatio-temporal expression of MKRN in seeds of pea and rice was performed using non radioactive mRNA in situ hybridization (NRISH) with DIG and BIOTIN labeled probes for pea and rice embryos respectively. Images of MKRN1 expression in e10.5 whole mount mouse embryo, hybridized with DIG labeled probes, were obtained from the Mouse Genome Database (MGD). MKRN transcripts were expressed in the vascular bundle, root apical meristem (RAM) and shoot apical meristem (SAM) in pea and rice embryos. The spatial annotation of the MKRN1 NRISH of whole mount mouse embryo shows prominent localization of MKRN1 in the brain, and its possible expression in spinal cord and the genital ridge. Localization of MKRN in the anterior and posterior ends of pea and rice embryo suggests to the probable role it may have in sculpting the pea and rice plants. The expression of MKRN in RAM may give a molecular insight into the hypothesis that plants have their brains seated in the root. The expression of MKRN is similar in functionally and anatomically analogous regions of plant and animal embryos, including the vascular bundle (spinal cord), the RAM (brain), and SAM (genital ridge) thus paving way for further inter-kingdom comparison studies.