Figure 7.

Identification of a conserved DNA sequence element with homology to a CTCF consensus sequence in mammalian DXZ4. (a) Schematic representation of a mouse Dxz4 monomer. The green arrowhead indicates the spliced exon. The blue vertical bars indicate repeat-masked sequence. The black bar represents the VNTR. The yellow box within the VNTR (bases 919 to 1,061) represents the conserved Dxz4 sequence. This sequence was used to align to the corresponding sequences from the mammals listed to generate the cladogram. The tree image was generated with MUSCLE version 3.8 [72] and ClustalW2 [73]. Classification of the groups is given to the right. (b) Schematic representation of a mouse Dxz4 monomer as above. The yellow box within the VNTR (bases 978 to 1,011) represents the DNA sequence that contains nucleotides invariable in all mammalian DXZ4 sequences assessed. This 34-bp sequence from each mammal was used to generate the position weight matrix through WebLogo [55]. Beneath the matrix is a previously determined Ctcf consensus sequence that is adapted from Martin et al. [47]. Note that the position weight matrix is the reverse complement of that shown in the referenced manuscript.

Horakova et al. Genome Biology 2012 13:R70   doi:10.1186/gb-2012-13-8-r70
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