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A homeobox is about 180 base pairs long; it encodes a protein domain (the homeodomain) which can bind DNA. Homeobox genes encode transcription factors which typically switch on cascades of other genes, for instance all the ones needed to make a leg. The homeodomain binds DNA in a specific manner. However, the specificity of a single homeodomain protein is usually not enough to recognize only its desired target genes. Most of the time, homeodomain proteins act in the promoter region of their target genes as complexes with other transcription factors, often also homeodomain proteins. Such complexes have a much higher target specificity than a single homeodomain protein.

A particular subgroup of homeobox genes are the Hox genes, which are found in a special gene cluster, the HOX cluster. Hox genes function in patterning the body axis. Thus, by providing the identity of particular body regions, Hox genes determine where limbs and other body segments will grow in a developing fetus or larva.

The homeobox genes were first found in the fruit fly Drosophila melanogasterDrosophila melanogaster Drosophila subobscura Drosophila ( Greek , drosos " dew", + phila "loving") is a genus of fruit fly however, members of Drosophila are more appropriately termed vinegar flies, wine flies, pomace flies, grape flies, and picked fruit and have subsequently been identified in many other species, from insectSubclass Apterygota Symphypleona globular springtails Subclass Archaeognatha (jumping bristletails) Subclass Dicondylia Monura extinct Thysanura (common bristletails) Subclass Pterygota Palaeodictyoptera extinct Ephemeroptera (mayflies) Odonata ( dragonfls to reptileCrocodilia Crocodilians Rhynchocephalia Tuataras Squamata Suborder Sauria Lizards Suborder Serpentes Snakes Testudines Turtles Superorder Dinosauria Saurischia Ornithischia The reptiles are a group of vertebrate animals. Most reptiles are tetrapods, and ts and mammalSubclass Monotremata Monotremata Subclass Marsupialia Didelphimorphia Paucituberculata Microbiotheria Dasyuromorphia Peramelemorphia Notoryctemorphia Diprotodontia Subclass Placentalia Xenarthra Dermoptera Desmostylia Scandentia Primates Rodentia Lagomorps. The diagram to the right is a structural model of the Rattus norvegicus Pit-1 homeobox-containing protein (purple) bound to DNA. Pit-1 is a regulator of growth hormoneGrowth hormone is a polypeptide hormone secreted by the anterior pituitary gland which stimulates growth and cell reproduction in humans and other vertebrate animals. This article describes human growth hormone physiology, with brief mentions of the disea gene transcription. Pit-1 is a member of the POU DNA-binding domain family of transcription factors so it can bind to DNA using both the POU domain and the homeodomain. Homeobox genes have even been found in fungi, for example the one-cellular yeastSaccharomyces cerevisiae is a yeast used in both baking and brewing. Yeast are a group of unicellular fungi a few species of which are commonly used to leaven bread and ferment alcoholic beverages. Most yeasts belong to the division Ascomycota. A few yeass and plants. This suggests that this gene family evolved very early and that the basic mechanisms of morphogenesis are the same for many organisms.

In analogy to computing one can think of homeobox sequence like a call to a subprogram. They switch on the production of a whole subsystem. The code for this must already be present in the DNA.

Mutations to homeobox genes can produce easily visible phenotypic changes. Two examples of homeobox mutations in the above-mentioned fruit fly are legs where the antennae should be, and a second pair of wings. Duplication of homeobox genes can produce new body segments, and such duplications are likely to have been important in the evolution of segmented animals.

See also: Evolutionary developmental biology