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This motif is bound and activated by the Paired- and LIM-type homeodomain proteins CEH-10 and TTX-3.
However, the RGD concentration is "locally enriched" in the vicinity of neighboring integrin αvβ3 once the first RGD motif is bound.
Although the structure of a TOS-Raptor complex is not yet known, the conservation might imply that the motif is bound in a sandwiched pocket.
According to [ 42], this motif is bound by transcription factor Msn2p and its close homologue Msn4p (referred to as Msn2/4p), which under nonstress conditions are located in the cytoplasm.
To test whether this motif is bound in vivo by Xpp1, we performed a dimethyl sulfate (DMS -induced in vivo footprint comparing the xpp1 DMS -inducedain and its parent strain.
In its unphosphorylated state this motif is bound to the medium-chain subunit AP-50 of the AP-2 clathrin adapter [ 12, 13], leading to the rapid endocytosis of CTLA-4.
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One element (5'- AGGAAGAG- 3') was found in 36% of the control fragments, but only 5% (5/103) of the fragments contained a DBE-like element (Table S2), indicating that the DBE and over-represented GAC/GAA/TG motif were bound specifically by rAc-DAF-16 DBD.
Both sequences matching the motif were bound by MrpC2, but the sequence in between and containing only half of each match to the motif was not bound.
Furthermore, genome-wide comparisons indicate that 50% of TAL1 peaks containing a Runx motif are bound by RUNX1/3 in Jurkat cells while 65% of TAL1 peaks containing an Ets motif are bound by ETS1.
It is not clear if the additional motifs (20-/26-mer 20-/26-mer 20-/26-mer the catonical mothe arightund by CTCF or by a co-factor.
Similarly, 18% of the ~20,000 AP-1 motifs that are within 150-bps of a second AP-1 motif are bound by c-Jun (Additional file 1: Figure S5B).
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