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The organization of cells in space at the appropriate time so that a correctly organized embryo forms. Pattern formation defines the main body axes of the developing embryo. In animals with a head and a tail these are: anterior/posterior, dorsal/ventral, right/left. The left-right axis in bilaterally symmetric animals looks the same on the outside but internally there are distinct differences between the two sides. In vertebrates, for example the heart is often on the left side. In animals, cells are also organized into different germ layers at the same time that axes formation occurs, The germ layers are: endoderm, mesoderm, and ectoderm. As development proceeds, these germ layers acquire different identities and give rise to different tissues and organs. In plants pattern formation produces the main body axes of the plant. apical-basal axis and radial axis. The apical-basal axis extends from the top of the shoot to the tip of the root.

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