DNA Binding Motif

						

			
Accessions: UP00264A_4 (UniPROBE 20160601)

			
Names: early retinoic acid, Early retinoic acid 1, Era-1, ERA1, homeo box A1, Homeobox protein Hox-A1, Homeoboxless protein ERA-1-399, Homeotic protein ERA-1-993, Hox-1.6, Hoxa-1, Hoxa1
Organisms: Mus musculus
Libraries: UniPROBE 20160601 1
1 Hume MA, Barrera LA, Gisselbrecht SS, Bulyk ML. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res : (2015). [Pubmed]
Length: 16
Consensus: ctrarcTAATTAmyky
Weblogo: 
PSSM: P0      A      C      G      T
01   0.19   0.42   0.19   0.21      c
02   0.14   0.15   0.06   0.65      t
03   0.27   0.13   0.47   0.14      r
04   0.62   0.10   0.15   0.13      a
05   0.27   0.08   0.61   0.05      r
06   0.08   0.53   0.22   0.17      c
07   0.01   0.03      0   0.97      T
08   0.96   0.03   0.01      0      A
09   0.99      0      0      0      A
10   0.01      0      0   0.99      T
11      0      0   0.01   0.99      T
12   0.96      0   0.04      0      A
13   0.28   0.48   0.17   0.07      m
14   0.14   0.45   0.14   0.27      y
15   0.11   0.17   0.41   0.31      k
16   0.06   0.30   0.18   0.46      y
Binding TFs: UP00264A (Homeobox domain)
Binding Sites: TAATAAAA
AATAAAAT
AATTAATA
ATAATAAA
ATTAATTA
ATTTTATG
CAATAAAA
CCATAAAA
GCAATAAA
GCAATTAA
GTAATAAA
GTAATTAA
GTCATAAA
GTCATTAA
GTCGTAAA
TAATTAAA
TCATAAAA
TCATTAAA
TCGTAAAA
TTAATTAA
			
Publications: Berger M.F, Badis G, Gehrke A.R, Talukder S, Philippakis A.A, Peña-Castillo L, Alleyne T.M, Mnaimneh S, Botvinnik O.B, Chan E.T, Khalid F, Zhang W, Newburger D, Jaeger S.A, Morris Q.D, Bulyk M.L, Hughes T.R. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133:1266-76 (2008). [Pubmed]

	
			


			

				

				
				
				
				

			

			

		

	
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