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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) ungulate or hoofed mammal, as well as the smallest extant even-toed ungulate.<ref name=eof5/><ref name=erythrocytes9>{{cite journal|last1=Fukuta|first1=K.|last2=Kudo|first2=H|last3=Jalaludin|first3=S.|year=1996|title=Unique pits on the erythrocytes of the lesser mouse-deer, Tragulus javanicus|journal=Journal of Anatomy|volume=189|issue=1|pages=211–213|pmc=1167845|pmid=8771414}}</ref><ref name=JoB/> The weight of the Java mouse-deer ranges from {{Convert|1|to|2|kg}}, with males being heavier than females. It has an average tail length of about {{Convert|5|cm|abbr=on}}. Mouse-deer are thought to be the most primitive [[ruminant]]s based on their behaviour and the [[fossil]] record, thus they are the living link between ruminants and non-ruminants.<ref name=animalrecs10>Carwardine, M., & London, E. (2007). Animal records. New York: Sterling</ref><ref name=JoB>{{Cite journal|last=Matsubayashi|first=Hisashi|last2=Bosi|first2=Edwin|last3=Kohshima|first3=Shiro|date=28 February 2003|title=Activity and Habitat Use of Lesser Mouse-Deer (Tragalus javanicus)
The Java mouse-deer is [[endotherm]]ic 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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