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

GTGTCCCGTATTATTATGCTGATCCCTACCGGAACCAGCGTCGGTCTGACCAGCGTCAGCCTTGGCGTGATCCGTGCAATGGAACGCAAAGGCGTTCGTC
TGAGCGTTTTCAAACCTATCGCTCAGCCGCGTACCGGTGGCGATGCGCCCGATCAGACTACGACTATCGTGCGTGCGAACTCTTCCACCACGACGGCCGC
TGAACCGCTGAAAATGAGCTACGTTGAAGGTCTGCTTTCCAGCAATCAGAAAGATGTGCTGATGGAAGAGATCGTCGCAAACTACCACGCTAACACCAAA
GACGCTGAAGTCGTTCTGGTTGAAGGTCTGGTCCCGACACGTAAGCACCAGTTTGCCCAGTCTCTGAACTACGAAATCGCTAAAACGCTGAATGCGGAAA
TCGTCTTCGTTATGTCTCAGGGCACTGACACCCCGGAACAGCTGAAAGAGCGTATCGAACTGACCCGCAACAGCTTCGGCGGTGCCAAAAACACCAACAT
CACCGGCGTTATCGTTAACAAACTGAACGCACCGGTTGATGAACAGGGTCGTACTCGCCCGGATCTGTCCGAGATTTTCGACGACTCTTCCAAAGCTAAA
GTAAACAATGTTGATCCGGCGAAGCTGCAAGAATCCAGCCCGCTGCCGGTTCTCGGCGCTGTGCCGTGGAGCTTTGACCTGATCGCGACTCGTGCGATCG
ATATGGCTCGCCACCTGAATGCGACCATCATCAACGAAGGCGACATCAATACTCGCCGCGTTAAATCCGTCACTTTCTGCGCACGCAGCATTCCGCACAT
GCTGGAGCACTTCCGTGCCGGTTCTCTGCTGGTGACTTCCGCAGACCGTCCTGACGTGCTGGTGGCCGCTTGCCTGGCAGCCATGAACGGCGTAGAAATC
GGTGCCCTGCTGCTGACTGGCGGTTACGAAATGGACGCGCGCATTTCTAAACTGTGCGAACGTGCTTTCGCTACCGGCCTGCCGGTATTTATGGTGAACA
CCAACACCTGGCAGACCTCTCTGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAA
CTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCTGAGCGCAGCCGTCGTCTGTCTCCGCCTGCGTTCCGTTATCAGCTGACTGAACTTGCG
CGCAAAGCGGGCAAACGTATCGTACTGCCGGAAGGTGACGAACCGCGTACCGTTAAAGCAGCCGCTATCTGTGCTGAACGTGGTATCGCAACTTGCGTAC
TGCTGGGTAATCCGGCAGAGATCAACCGTGTTGCAGCGTCTCAGGGTGTAGAACTGGGTGCAGGGATTGAAATCGTTGATCCAGAAGTGGTTCGCGAAAG
CTATGTTGGTCGTCTGGTCGAACTGCGTAAGAACAAAGGCATGACCGAAACCGTTGCCCGCGAACAGCTGGAAGACAACGTGGTGCTCGGTACGCTGATG
CTGGAACAGGATGAAGTTGATGGTCTGGTTTCCGGTGCTGTTCACACTACCGCAAACACCATCCGTCCGCCGCTGCAGCTGATCAAAACTGCACCGGGCA
GCTCCCTGGTATCTTCCGTGTTCTTCATGCTGCTGCCGGAACAGGTTTACGTTTACGGTGACTGTGCGATCAACCCGGATCCGACCGCTGAACAGCTGGC
AGAAATCGCGATTCAGTCCGCTGATTCCGCTGCGGCCTTCGGTATCGAACCGCGCGTTGCTATGCTCTCCTACTCCACCGGTACTTCTGGTGCAGGTAGC
GACGTAGAAAAAGTTCGCGAAGCAACTCGTCTGGCGCAGGAAAAACGTCCTGACCTGATGATCGACGGTCCGCTGCAGTACGACGCTGCGGTAATGGCTG
ACGTTGCGAAATCCAAAGCGCCGAACTCTCCGGTTGCAGGTCGCGCTACCGTGTTCATCTTCCCGGATCTGAACACCGGTAACACCACCTACAAAGCGGT
ACAGCGTTCTGCCGACCTGATCTCCATCGGGCCGATGCTGCAGGGTATGCGCAAGCCGGTTAACGACCTGTCCCGTGGCGCACTGGTTGACGATATCGTC
TACACCATCGCGCTGACTGCGATTCAGTCTGCACAGCAGCAGTAA

Loop counts:

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

Tetra-loop variants:

CUGA    1
UCCC    1
CUCC    1
AUAU    1
ACCA    1
AACA    1
UCUG    1
GAAC    1

Single bulge variants:

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

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