Annotated gene sequence

Experiment = cell-free 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

ATGGCGTGGAATCAGCCCGGTAATAACGGACAAGACCGCGACCCGTGGGGAAGCAGCAAACCTGGCGGCAACTCTGAGGGAAATGGAAACAAAGGCGGTC
GCGATCAAGGGCCACCTGATTTAGATGATATCTTCCGCAAACTGAGCAAAAAGCTCGGTGGTCTGGGCGGCGGTAAAGGCACCGGATCTGGCGGTGGCAG
TTCATCGCAAGGCCCGCGCCCGCAGCTTGGCGGTCGTGTCGTTACCATCGCAGCGGCAGCGATTGTCATTATCTGGGCGGCCAGTGGTTTCTATACCATT
AAAGAAGCCGAACGCGGCGTGGTAACACGCTTTGGTAAATTCAGCCATCTGGTTGAGCCGGGTCTGAACTGGAAACCGACGTTTATCGACGAAGTCAAAC
CGGTGAACGTGGAAGCCGTGCGTGAACTGGCCGCTTCTGGTGTGATGCTGACGTCGGACGAGAACGTAGTGCGCGTTGAGATGAACGTGCAGTACCGCGT
CACCAATCCGGAAAAATATCTGTATAGCGTGACCAGCCCGGATGACAGCCTGCGTCAGGCTACCGACAGCGCCCTGCGTGGAGTTATCGGTAAATACACC
ATGGACCGCATTCTGACGGAAGGTCGTACCGTGATTCGTAGCGATACTCAGCGCGAACTGGAAGAGACGATTCGTCCGTATGACATGGGTATCACGCTGC
TGGACGTCAACTTCCAGGCTGCTCGTCCGCCGGAAGAAGTAAAAGCGGCGTTTGACGATGCGATTGCCGCGCGTGAAAACGAACAGCAATACATTCGTGA
AGCAGAAGCGTATACCAACGAAGTTCAGCCGCGTGCGAACGGTCAGGCGCAACGTATCCTCGAAGAGGCGCGTGCGTACAAGGCCCAGACCATCCTGGAA
GCTCAGGGTGAAGTGGCGCGCTTTGCTAAACTTCTGCCGGAATATAAAGCCGCGCCGGAAATTACTCGCGAGCGTCTGTATATCGAGACGATGGAAAAAG
TGTTGGGTAACACCCGCAAAGTGCTGGTTAACGATAAAGGTGGCAACCTGATGGTTCTGCCGTTAGACCAGATGCTGAAAGGTGGTAACGCCCCTGCGGC
GAAGAGCGATAACGGTGCCAGCAATCTGCTGCGTCTGCCGCCAGCCTCTTCCTCCACAACCAGTGGAGCAAGCAACACGTCGTCCACCAGTCAGGGCGAT
ATTATGGACCAACGCCGCGCCAACGCGCAGCGTAACGACTACCAGCGTCAGGGGGAATAA

Loop counts:

3 nts: 2
4 nts: 5
5 nts: 2
6 nts: 1
7 nts: 2
8 nts: 2

Tetra-loop variants:

UGAU    1
CAAC    1
AUCU    1
GAAA    1
AAGC    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 1
U x 0 bulge: 0
C x 0 bulge: 2

1 x 1 internal loop variants:

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