SRPECLI_BZCN_0004

Construct

RMDB ID

SRPECLI_BZCN_0004

Name

SRP RNA, E. coli

Sequence (125 nt)

AUCGGGGGCUCUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCCCCCACCCGGGUCGGC

Structure

.............................................................................................................................

Offset

-3

# of constructs

97

# of data points

7344

Last modified

11/10/17

Version

2

Owner

Julius Lucks

Comments

REACTIVITY and READS are stored below in groups for each replicate. Reactivity is first, then positive reads, followed by unmodified reads
Reactivities are reported as rhos
rho_i = theta_i * L, where L = length of RNA sequence
See Aviran, S., Lucks, J.B., and Pachter, L. (doi:10.1109/Allerton.2011.6120379) for theta_i and beta_i reactivity definitions
Data from Watters et al., "Cotranscriptional Folding of a Riboswitch at Nucleotide Resolution" Nature Structural & Molecular Biology (doi: 10.1038/nsmb.3316)
Linker sequences have been removed
Cotranscriptionally folded E. coli SRP, 30 seconds of transcription, then refolded at equilibrium in the transcription buffer
Sequence taken directly from Wong, et al. "Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures" (doi:10.1073/pnas.0705038104)

Annotation

• experiment: cotranscriptional SHAPE-Seq
• modifier: BzCN
• chemical: Tris-acetate:20mM (pH8.0) chemical:MgCl2:5mM chemical:EDTA:0.1mM chemical:DTT:1mM chemical:KCl:50mM chemical:NTPs:200uM chemical:BSA:1mg/mL temperature:37C