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

ATGACCAACATCACCAAGAGAAGTTTAGTAGCAGCTGGCGTTCTGGCTGCGCTAATGGCAGGGAATGTCGCGCTGGCAGCTGATGTACCCGCAGGCGTCA
CACTGGCGGAAAAACAAACACTGGTACGTAACAATGGTTCAGAAGTTCAGTCATTAGATCCGCACAAAATTGAAGGTGTTCCGGAGTCTAATATCAGCCG
AGACCTGTTTGAAGGCTTACTGGTCAGCGATCTTGACGGTCATCCAGCACCTGGCGTCGCTGAATCCTGGGATAATAAAGACGCGAAAGTCTGGACCTTC
CATTTGCGTAAAGATGCGAAATGGTCTGATGGCACGCCAGTCACAGCACAAGACTTTGTGTATAGCTGGCAACGTTCTGTTGATCCGAACACTGCTTCTC
CGTATGCCAGTTATCTGCAATATGGGCATATCGCCGGTATTGATGAAATTCTTGAAGGGAAAAAACCGATTACCGATCTCGGCGTGAAAGCTATTGATGA
TCACACATTAGAAGTCACCTTAAGTGAACCCGTTCCGTACTTCTATAAATTACTTGTTCACCCATCAACTTCACCGGTGCCAAAAGCCGCTATCGAGAAA
TTCGGCGAAAAATGGACCCAGCCTGGTAATATCGTCACCAACGGTGCCTATACCTTAAAAGATTGGGTCGTAAACGAACGAATCGTTCTTGAACGCAGCC
CGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAAT
CGACATGACGAATAACAGCATGCCGATCGAATTGTTCCAGAAGCTGAAAAAAGAGATCCCGGACGAAGTTCACGTTGATCCATACCTGTGCACTTACTAT
TACGAAATTAACAACCAGAAACCGCCATTCAACGATGTGCGTGTGCGTACCGCACTGAAACTAGGTATGGACCGCGATATCATTGTTAATAAAGTGAAAG
CGCAGGGCAACATGCCCGCCTATGGTTACACTCCACCGTATACTGATGGCGCAAAATTGACTCAGCCAGAATGGTTTGGCTGGAGCCAGGAAAAACGTAA
CGAAGAAGCGAAAAAACTGCTGGCTGAAGCGGGTTATACCGCAGACAAACCGTTGACCATCAACCTGTTGTATAACACCTCCGATCTGCATAAAAAGCTG
GCGATTGCTGCCTCTTCATTGTGGAAGAAAAACATTGGTGTAAACGTCAAACTGGTTAACCAGGAGTGGAAAACGTTCCTCGACACCCGTCACCAGGGTA
CTTTTGATGTGGCCCGTGCAGGCTGGTGTGCTGACTACAACGAACCAACTTCCTTCCTGAACACCATGCTTTCGAACAGCTCGATGAATACCGCGCATTA
TAAGAGCCCGGCCTTTGACAGCATTATGGCGGAAACGCTGAAAGTGACTGACGAGGCGCAGCGCACAGCTCTGTACACTAAAGCAGAACAACAGCTGGAT
AAGGATTCGGCCATTGTTCCTGTTTATTACTACGTGAATGCGCGTCTGGTGAAACCGTGGGTTGGTGGCTATACCGGCAAAGATCCGCTGGATAATACCT
ATACCCGGAATATGTACATTGTGAAGCACTAA

Loop counts:

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

Tetra-loop variants:

GAAA    1
AAGG    1
GACU    1
CGUU    1

Single bulge variants:

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

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