In the Ennead cosmogeny, he was considered to be the first god, having arisen by his own force himself, sitting on a mound (benben), from the primordial waters (Nu). Early myths state that Atum created the god Shu and goddess Tefnut from his semen by masturbation in the city of Annu (the Egyptian name for Heliopolis), a belief strongly associated with Atum's nature as an hermaphrodite (his name meaning completeness). Strictly, the myth states that Atum ejaculated his Semen into his mouth, impregnating himself, possibly indicating autofellatio, which has lead many to misinterpret (euphemistically) the myth as indicating creation from mucus).

Later belief held that Shu and Tefnut were created by Atum having sex with his shadow, which was referred to as Iusaaset (also spelt Juesaes, Ausaas, Iusas, and Jusas, and in Greek as Saosis), meaning (the) great (one who) comes forth. Consequently, Iusaaset was seen as the mother and grandmother of the gods. The strength, hardiness, medical properties, and edibility, lead the acacia tree to be considered the tree of life, and thus the oldest, which was situated close to, and north of, Heliopolis, was said to be the birthplace of the gods. Thus, as the mother, and grandmother, of the gods, Iusaaset was said to own this tree.

In art, Atum was always considered as a man, enthroned, or sometimes standing, and depicted wearing both the crown of Upper Egypt, and that of Lower Egypt. In his later form as the setting sun, as opposed to Nefertum, Atum was depicted in the same manner but as an aged man. However, it was sometimes said that Atum was originally a serpent, a form to which he was said to be destined to return when the world ends, only changing into a human during its existence.

In later years, the Ennead mythos, and an alternative mythos, that of the Ogdoad, merged, and since Ra, from the Ogdoad, was also the creator (in that system), and a solar deity, their two identities merged, into Atum-Ra. But as Ra was the whole sun, and Atum just the sun when it sets, it was Atum who was thought of as an aspect of Ra, and eventually subsumed into him. When this happened, his shadow, Iusaaset, was described as Rat, which is simply the feminine form of Ra. As both the cosmogeny associated with Ra and that of Atum said that the origin of each was the primordial waters, when, in later years, Neith came to embody these waters, Iusaaset became considered an aspect of Neith rather than Atum-Ra.

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