In the telomeric gene desert flanking the murine HoxD cluster, a 20 kb conserved region (CS38-39-40) is characterized by the presence of two ncRNAs. We analyzed their transcriptional profiles during limb development, in serial deletions affecting the HoxD cluster, enabling us to highlight competition between gene promoters for enhancers.We also analyzed 3D reallocations of CS38 (and other key loci), when duplicating the region between the two TADs (isolating the two flanking gene deserts from each other). Our experiments showed the presence of a strong boundary inside the cluster, responsible of the segregation in two TADs as well as the existence of two different territories in the limb; proximal and distal.Since CS38-39-40 is also characterized by the presence of three strong CTCF binding sites, likely to be responsible of anchor and enhancer capacities of this region, our work focused in a second time on establishing a line lacking the CTCF1a (located in CS38).