The CTCF-like protein, CTCFL, is a DNA-binding factor that regulates the transcriptional program of mammalian male germ cells. CTCFL consists of eleven zinc fingers flanked by polypeptides of unknown structure and function. We determined that the C-terminal fragment predominantly consists of extended and unordered content. Computational analysis predicts that the N-terminal segment is also disordered. The molecular architecture of CTCFL may then be similar to that of its paralog, the CCCTC-binding factor, CTCF. We speculate that sequence divergence in the unstructured terminal segments results in differential recruitment of cofactors, perhaps defining the functional distinction between CTCF in somatic cells and CTCFL in the male germ line. (C) 2010 Elsevier Inc. All rights reserved.