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Mouse-deer possess a triangular-shaped head, arched back, and round body with elevated rear quarters. The thin, short legs which support the mouse-deer are about the diameter of an average pencil. Although Java mouse-deer do not possess antlers or horns like regular deer, male Java mouse-deer have elongated, tusk-like upper canines which protrude downward from the upper jaw along the sides of their mouth. Males use these “tusks” to defend themselves and their mates against rivals.<ref name=superhero8>Nowak, R., J. Paradiso. 1983. Walker's Mammals of the World. Chicago: Johns Hopkins University Press.</ref> Females can be distinguished from males because they lack these prominent canines, and they are slightly smaller than the males.<ref name=eof5/> Java mouse-deer can furthermore be distinguished by their lack of upper incisors. The coat coloration of the Java mouse-deer is reddish-brown with a white underside. Pale white spots or vertical markings are also present on the animal’s neck.<ref name=eof5/>
With an average length of {{Convert|45|cm|abbr=on}} and an average height of {{Convert|30|cm|abbr=on}}, the Java mouse-deer is the smallest [[Neontology|extant]] (living)
The Java mouse-deer is [[endothermic]] and [[homoeothermic]], and has an average basal metabolic rate of about 4.883 [[watt]]s.<ref name=eof5/> It also has the smallest [[red blood cell]]s (erythrocytes) of any mammal, and about 12.8% of the cells have pits on them. The pits range in diameter from 68 to 390 [[nanometre]]s. Red blood cells with pits are unique and have not been reported before either physiologically or pathologically.<ref name=erythrocytes9/>
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