The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein (eg Swiss:P10180).

1: Isoforms of hepatocyte nuclear factor-6 differ in DNA-binding properties, contain a bifunctional homeodomain, and define the new ONECUT class of homeodomain proteins. Lannoy VJ, Burglin TR, Rousseau GG, Lemaigre FP; J Biol Chem 1998;273:13552-13562. PMID:9593691

2: Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1. Yamasaki K, Akiba T, Yamasaki T, Harata K; Nucleic Acids Res. 2007;35:5073-5084. PMID:17652321