Fig. 2. Structural classification of Hox clusters. Type O (organized) clusters are well organized, with genes tightly arranged and all encoded by the same DNA strand. They are devoid of both `foreign' genes and repeats, yet they may contain non-coding RNAs and miRNAs. Vertebrate clusters provide, so far, the sole example of this organization. Type D (disorganized) clusters are much larger and may contain mixed-up Hox genes (black boxes), or genes in opposite orientations, in addition to non-Hox genes (white boxes) and repeats. Type D examples are found in amphioxus and in sea urchins. Split (type S) clusters can have type O or type D features in each of their sub-clusters, such as in Diptera, whereas the type A (atomized) `cluster' represents the `no-cluster' situation, in which genes are found, at best, in pairs at scattered genomic loci (e.g. in Oikopleura).