BSUGLY_DMS_0013

Construct

RMDB ID

BSUGLY_DMS_0013

Name

Bacillus subtilis gcvT glycine riboswitch delta P0 variant, cotranscriptionally folded, 0 mM glycine

Sequence (265 nt)

AGCAAGGGGAGAGACCUGACCGAAAACCUCGGGAUACAGGCGCCGAAGGAGCAAACUGCGGAGUGAAUCUCUCAGGCAAAAGAACUCUUGCUCGACGCAACUCUGGAGAGUGUUUGUGCGGAUGCGCAAACCACCAAAGGGGACGUCUUUGCGUAUGCAAAGUAAACUUUCAGGUGCCAGGACAGAGAACCUUCAUUUUACAUGAGGUGUUUCUCUGUCCUUUUUUGUAUCCUGAUUCGUCAGGCGAUGUGUGCUGGAAGACAUU

Structure

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

Offset

0

# of constructs

247

# of data points

35055

Last modified

05/20/25

Version

1

Owner

Eric Strobel

Comments

Sequencing reads were demultiplexed by transcript length and channel using the TECtools cotrans_preprocessor script
Neighboring transcript smoothing was applied
Mutation mapping and reactivity calculation was performed using shapemapper2 (Busan and Weeks,  DOI: 10.1261/rna.061945.117)
Reactivity values were normalized as described in section 3.2.1 of Low and Weeks, 2010, DOI: 10.1016/j.ymeth.2010.06.007
The leading SC1 hairpin sequence (5-ATGGCCTTCGGGCCAA), which is masked by a primer, was trimmed
Transcripts from 223 to 250 and after 254 were not enriched by template DNA strand biotin-streptavidin roadblocks and may be poor quality
Data are from two independent replicates that were analyzed separately then merged and normalized
True offset is -9, sequence begins at A10 due to deletion of the first 9 nucleotides

Annotation

• experiment: TECprobe-VL
• modifier: DMS
• temperature: 37C
• chemical: Tris-HCl:100mM (pH8.0), KCl:50mM, EDTA:0.1mM, DTT:1mM, MgCl2:10mM, NTPs:50uM, BSA:0.1mg/mL, glycine:none