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

ATGAGTGAGGCAGAAGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGC
CGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCCAGTGCAACCTGCGTTTCGA
CGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCC
TCCGATTATTTTGATCAGCTCCACGCCTATGCGATCGAACTGATCAATAAAGGCCTGGCGTACGTTGATGAACTGACGCCGGAACAGATCCGCGAATACC
GCGGCACCCTGACGCAACCGGGTAAAAACAGCCCGTACCGCGACCGCAGCGTTGAAGAGAACCTGGCGCTGTTCGAAAAAATGCGTGCCGGTGGTTTTGA
AGAAGGTAAAGCCTGCCTGCGTGCGAAAATCGACATGGCTTCACCGTTTATCGTGATGCGCGATCCGGTGCTGTACCGTATTAAATTTGCTGAACACCAC
CAGACTGGCAACAAGTGGTGCATCTACCCGATGTACGACTTCACCCACTGCATCAGCGATGCCCTGGAAGGTATTACGCACTCTCTGTGTACGCTTGAGT
TCCAGGACAACCGTCGTCTGTACGACTGGGTACTGGACAACATCACGATTCCTGTTCACCCGCGCCAGTATGAGTTCTCGCGCCTGAATCTGGAATACAC
CGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGT
GGTTACACTGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTGACCAAGCAGGACAACACCATTGAGATGGCGTCGCTGGAATCCTGCATCCGTG
AAGATCTCAACGAAAATGCGCCGCGCGCAATGGCGGTTATCGATCCGGTGAAACTGGTTATCGAAAACTATCAGGGCGAAGGCGAAATGGTTACCATGCC
GAACCATCCGAACAAACCGGAAATGGGCAGCCGTCAGGTGCCGTTTAGCGGTGAGATTTGGATTGATCGCGCCGATTTCCGCGAAGAAGCTAACAAGCAG
TACAAACGTCTGGTGCTGGGTAAAGAAGTGCGTCTGCGTAATGCTTATGTGATTAAGGCAGAACGCGTCGAGAAAGATGCCGAAGGTAATATCACCACCA
TCTTCTGTACTTATGACGCCGATACCTTAAGCAAAGATCCGGCAGATGGTCGTAAAGTCAAAGGTGTTATTCACTGGGTGAGCGCGGCACATGCGCTGCC
GGTTGAAATCCGTTTGTATGACCGTCTGTTCAGCGTGCCTAACCCAGGTGCTGCGGATGATTTCCTGTCGGTGATTAACCCGGAATCGCTGGTGATCAAA
CAGGGCTTTGCTGAACCGTCGCTGAAAGATGCGGTTGCGGGTAAAGCATTCCAGTTTGAGCGTGAAGGTTACTTCTGCCTCGATAGCCGCCATTCTACGG
CGGAAAAACCGGTATTTAACCGCACCGTTGGGCTGCGTGATACCTGGGCGAAAGTAGGCGAGTAA

Loop counts:

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

Tetra-loop variants:

GCAG    1
UUAU    1
GUUA    1
GUUG    1
GUCC    1
CUAU    1
CUGU    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 0
U x 0 bulge: 4
C x 0 bulge: 1

1 x 1 internal loop 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: 3
U x G bulge: 0
U x A bulge: 0
U x U bulge: 0
U x C bulge: 1
C x G bulge: 0
C x A bulge: 3
C x U bulge: 1
C x C bulge: 0