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

Accession R0505
Feature Type Riboswitch
Name Lysine riboswitch
Regulatory Motif
(RNAMotif descriptor)
descr

	h5(minlen=3, maxlen=8, seq="AG$")

		ss(minlen=4, maxlen=5, seq="^AGG")

		h5(minlen=7, maxlen=9, seq="^GC")

			ss(seq="^A$")

			ss(minlen=2, maxlen=3)

			ss(seq="^AGUA$")

			ss(minlen=0, maxlen=2)

			h5(minlen=4, maxlen=9)

				ss(minlen=0, maxlen=4)

				ss(seq="^G$")

				ss(minlen=0, maxlen=1)

				ss(seq="^AG$")

				ss(minlen=0, maxlen=2)

				h5(minlen=0, maxlen=2)

					ss(minlen=3, maxlen=15)

				h3

				ss(minlen=0, maxlen=7)

			h3

			ss(minlen=0, maxlen=3)

			ss(seq="^AAAGG$")

		h3

		ss(seq="^CGA$")

		h5(minlen=2, maxlen=17, seq="U$")

			ss(minlen=7, maxlen=13)

		h3

		h5(minlen=9, maxlen=10, seq="^GG")

			ss(minlen=0, maxlen=5)

			ss(seq="^AA$")

			ss(minlen=1, maxlen=2)

		h3

		ss(seq="^G$")

		h5(minlen=5, maxlen=12, seq="^UCA")

			ss(minlen=2, maxlen=9)

		h3

		ss(len=4, seq="^AG")

	h3
Ligand Lysine
References Winkler WC, and Breaker RR
Genetic control by metabolite-binding riboswitches.
Chembiochem 2003; 4(10), 1024-32   PubMed 

Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, and Breaker RR
An mRNA structure in bacteria that controls gene expression by binding lysine.
Genes Dev 2003; 17(21), 2688-97   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