Properties of L. camtschaticum CTCF and CTCF2 genes. (a) Protein domain structures, in comparison with human CTCF and CTCFL. The Zn finger domains (ZF) were identified by MOTIF Search (http://www.genome.jp/tools/motif/). See SI Materials and Methods for detail procedures of LjCTCF and LjCTCF2 sequence determination by cDNA cloning. (b) Expression levels of LjCTCF (white) and LjCTCF2 (black) in embryos and adult tissues. FPKM, fragments per kilobase of exon per million mapped sequence reads. (c) Whole-mount in situ hybridization on stage 26.5 embryos. Riboprobes were designed in non-conserved regions downstream to the Zn finger domains to avoid cross-hybridization (for the magnified view and the result with upstream riboprobes, see Supplementary Fig. S10). Note that the difference in the intensities of the expression signals between the two genes do not correspond to that of actual expression levels, as indicated by our RNA-seq data in (b). Scale bars: 500 μm. (d) Molecular phylogenetic tree. This tree was inferred with the maximum-likelihood approach using 208 aligned amino acid sites (see Supplementary Tables S8 and S9 for the list of sequences used). Two stickleback sequences are included (upper, Ensembl ENSGACP00000003270; lower, ENSGACP00000020939). At each branch node in the tree, only bootstrap value of no less than 60, and the posterior probability inferred with the Bayesian approaches are shown.