Annotated gene sequence

Experiment = in-cell SHAPE/ 1M7 Cell = MG1655 Original Data Reference = Cell. 2018;173(1):181-195.e18.

stable secondary structure loop bulge/internal loop no SHAPE data coding sequence

ATGGGTCAGAAAGTACATCCTAATGGTATTCGCCTGGGTATTGTAAAACCATGGAACTCTACCTGGTTTGCGAACACCAAAGAATTCGCTGACAACCTGG
ACAGCGATTTTAAAGTACGTCAGTACCTGACTAAGGAACTGGCTAAAGCGTCCGTATCTCGTATCGTTATCGAGCGTCCGGCTAAGAGCATCCGTGTAAC
CATTCACACTGCTCGCCCGGGTATCGTTATCGGTAAAAAAGGTGAAGACGTAGAAAAACTGCGTAAGGTCGTAGCGGACATCGCTGGCGTTCCTGCACAG
ATCAACATCGCCGAAGTTCGTAAGCCTGAACTGGACGCAAAACTGGTTGCTGACAGCATCACTTCTCAGCTGGAACGTCGCGTTATGTTCCGTCGTGCTA
TGAAGCGTGCTGTACAGAACGCAATGCGTCTGGGCGCTAAAGGTATTAAAGTTGAAGTTAGCGGCCGTCTGGGCGGCGCGGAAATCGCACGTACCGAATG
GTACCGCGAAGGTCGCGTACCGCTGCACACTCTGCGTGCTGACATCGACTACAACACCTCTGAAGCGCACACCACTTACGGTGTAATCGGCGTTAAAGTG
TGGATCTTCAAAGGCGAGATCCTGGGTGGTATGGCTGCTGTTGAACAACCGGAAAAACCGGCTGCTCAGCCTAAAAAGCAGCAGCGTAAAGGCCGTAAAT
AA

Loop counts:

4 nts: 1
5 nts: 2
6 nts: 2

Tetra-loop variants:

GAAU    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 1
U x 0 bulge: 0
C x 0 bulge: 0

1 x 1 bulge variants:

G x G bulge: 0
G x A bulge: 0
G x U bulge: 0
G x C bulge: 0
A x G bulge: 0
A x A bulge: 1
A x U bulge: 0
A x C bulge: 0
U x G bulge: 0
U x A bulge: 0
U x U bulge: 0
U x C bulge: 0
C x G bulge: 0
C x A bulge: 0
C x U bulge: 0
C x C bulge: 0