Classification of deduced amino acid sequence revealed that red sea bream and yellowtail CSD showed 88.8% homology similar to Nile tilapia, platyfish, etc. Domain analysis shows that pyridoxine binding region was conserved in CSD from both species.
The tRNAAsp binding residues at anti-codon binding region are conserved among the three organisms and showed less variations.
However, most of the Ski binding region is conserved between all three Gli proteins, suggesting that Ski binding and HDAC recruitment is part of a general transcription termination signal common to all Gli proteins.
To test whether the C-terminal U4/U6 di-snRNA-binding region is conserved in yPrp3, we produced a protein comprising the 177 C-terminal residues of yPrp3 (residue 296 469; yPrp3CTF).
Despite that it was often impossible to establish whether particular [G CG N]4 motifs within DCC binding regions were evolutionary conserved, we were able to detect 894 sites in D. virilis.
In the Fgfr2 locus, four p63 binding regions were evolutionary conserved in mouse and were enriched for histone H3 methylation on lysine 4 mono- and di-methylations (H3K4me1 and me2), chromatin marks known to associate with distal regulatory regions [reviewed in (Bell et al, 2011)], suggesting that they function as regulatory elements (Supporting Information Fig S7A).
This ARF-binding disordered region is conserved across the GAT domains of human GGAs, as demonstrated earlier.
Remarkably even though the genetic load region around this ParB site seems a spot for insertions of gene sequences, the ParB binding site in the genetic load region was conserved in all three conjugative plasmids, suggesting an important function for this region.
In order to increase support for the computationally found binding sites, we performed cross-species comparison and indicated promoter binding regions that were conserved.
Six p63-binding regions that were conserved between human and mouse were tested by ChIP-qPCR in primary mouse keratinocytes (Supplementary Material, Table S1).
