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For example, out of tens of thousands of known human and mouse genes, there are only 158 binding motifs for human and 148 for mouse in two well-known databases (i.e., JASPAR [ 18] and TRANSFAC [ 19]), respectively.
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Among these we find 8 out of the 18 human DYNLL binding motifs for which the binding site had already been identified.
The presence of consensus binding motifs for RAX, an rx3 ortholog in humans, was sought in 5 kb promoter regions of selected zebrafish genes.
We also describe uncommon positioning of binding motifs for several T-cell lineage specific factors in human promoters.
For instance, the LTR-derived promoter significantly increases the expression of human EBR gene in placenta (Medstrand et al. 2001), and Alu elements provide binding motifs for three zinc-finger TFs (Sp1, estrogen receptor alpha, and YY1) (Oei et al. 2004).
Like humans, mouse L1 also has a TATA-less promoter that might require transcription factors binding motifs for its transcriptional initiation.
KorA carried a binding motif for coenzyme A, and KorB carried binding motifs for Fe-S cluster and thiamine pyrophosphate.
The TTGGCAAATA motif appears to resemble overlapping binding motifs for NFI, FoxA1 and Oct-1 (Figure 4C).
Fourteen conserved promoter motifs were identified, seven of which shared significant similarity with binding motifs for previously characterized regulators [25].
DREME is capable for finding binding motifs for cofactor TFs.
This approach has been successfully applied to determine a binding motif for the chemokine receptor CXCR4.
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