RegRNA
A Regulatory RNA Motifs and Elements Finder
  Release 1.0, Jan 2006
 
 
 

Accession R0501
Feature Type Riboswitch
Name Coenzyme-B12 riboswitch
Regulatory Motif
(RNAMotif descriptor)
descr

	ss(minlen=1, maxlen=3, seq="^G")

	h5(minlen=2, maxlen=3)

		h5(seq="^GGU$")

			ss(minlen=0, maxlen=1)

			h5(minlen=2, maxlen=5)

				ss(minlen=3, maxlen=4)

			h3

			ss(minlen=0, maxlen=2)

			ss(seq="^AA$")

			ss(minlen=0, maxlen=1)

			h5(seq="^AGG$")

				ss(seq="^GAA$")

				h5(minlen=3, maxlen=5, seq="GG$")

					ss(seq="^U$")

					ss(minlen=0, maxlen=3)

					ss(seq="^A$")

					ss(minlen=0, maxlen=2)

				h3

				ss(seq="^RC$")

				h5(minlen=0, maxlen=1)

					h5(seq="^GC$")

						ss(minlen=0, maxlen=2)

						ss(seq="^CCC$")

					h3

				h3

				ss(seq="^R$")

				h5(seq="^C$")

					h5(minlen=0, maxlen=1)

						h5(seq="^G$")

							ss(seq="^UR")

							ss(minlen=0, maxlen=1)

								h5(len=3, seq="R$")

									ss(minlen=3, maxlen=5)

									h5(minlen=7, maxlen=8)

										ss(minlen=0, maxlen=2)

										h5(minlen=0, maxlen=2)

											ss(minlen=0, maxlen=4)

										h3

										ss(minlen=0, maxlen=1)

										h5(len=3, seq="CC$")

											ss(seq="^A$")

												h5(minlen=5, maxlen=6, seq="^CUG")

													ss(minlen=3, maxlen=4)

												h3

											ss(seq="^GAA$")

										h3

									h3

									ss(len=3)

									h5(minlen=0, maxlen=5)

										ss(minlen=3, maxlen=7)

									h3

									ss(minlen=2, maxlen=4)

								h3

							ss(seq="^RAGY$")

						h3

					h3

				h3

				ss(seq="^RA$")

				ss(len=1)

				ss(seq="^A$")

			h3

		h3

	h3
Ligand Coenzyme B12 (adenosylcobalamin)
References Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, and Breaker RR
Genetic control by a metabolite binding mRNA.
Chem Biol 2002; 9(9), 1043   PubMed 

Winkler WC, and Breaker RR
Genetic control by metabolite-binding riboswitches.
Chembiochem 2003; 4(10), 1024-32   PubMed 

Nahvi A, Barrick JE, and Breaker RR
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.
Nucleic Acids Res 2004; 32(1), 143-50   PubMed 

Mandal M, and Breaker RR
Gene regulation by riboswitches.
Nat Rev Mol Cell Biol 2004; 5(6), 451-63   PubMed 


Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Taiwan
Contact with Dr. Hsien-Da Huang