Only 26% (30 of 117) of TF binding motifs, in which cardiac TFs such as MEF2A were included, were shared between tele- and proximal enhancers.
FBLM residues RPHPD are flanked on either end by hydrophobic residues and comprise the core of the Fn-binding motif in which charged residues alternate with proline residues.
The DH domain is related to the forkhead/winged-helix type of DNA-binding motifs in which the "wing" is a β-strand hairpin corresponding to strands β4 and β5 of the DHD, and where the "helix" corresponds to the α2 helix of the DHD.
The current version of YY1TargetDB contains 92 314 binding loci identified by ChIP-based experiments; 157 200 YY1-binding motifs in which 42 are experimentally verified and 157 158 are computationally predicted; and 130 759 binding motifs for 47 cofactors.
Both genes contain a paired CRE1 binding motif in their promoter, which would support this assumption.
Generally, 14-3-3s do not bind appreciably to unphosphorylated proteins, with the exception of the ExoS, which is injected into host mammalian cells by the pathogenic bacterium Pseudomonas aeruginosa and contains an novel binding motif GLLDALDLAS, in which the hydrophobic residues (Leu, Leu and Leu) are essential for binding to cellular 14-3-3s 14-3-3s 14-3-3ss [ 46, 47].
The RNA binding motif in YhjD is homologous to RNase BN, which is involved in tRNA processing [SSDB (Sequence Similarity DataBase) motif result, data not shown].
The metal binding motif in NgoL-CTD has the sequence DMHAAAERVNYE, which aligns well with the established consensus sequence of DQHA(X 2E(X)4E, and extends from residues 491 to 502.
Although the novel finding of the later is that the long noncoding RNA designated NKILA is upregulated by immunostimulants due to the presence of a NF-kB binding motif in the promoter region of this gene which is located in the human chromosome 20q13.31.
We also found a novel motif (AP4-L) which is similar to the V$AP4_01 binding motif in TRANSFAC.
