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

ATGAAAAACATCAATCCAACGCAGACCGCTGCCTGGCAGGCACTACAGAAACACTTCGATGAAATGAAAGACGTTACGATCGCCGATCTTTTTGCTAAAG
ACGGCGATCGTTTTTCTAAGTTCTCCGCAACCTTCGACGATCAGATGCTGGTGGATTACTCCAAAAACCGCATCACTGAAGAGACGCTGGCGAAATTACA
GGATCTGGCGAAAGAGTGCGATCTGGCGGGCGCGATTAAGTCGATGTTCTCTGGCGAGAAGATCAACCGCACTGAAAACCGCGCCGTGCTGCACGTAGCG
CTGCGTAACCGTAGCAATACCCCGATTTTGGTTGATGGCAAAGACGTAATGCCGGAAGTCAACGCGGTGCTGGAGAAGATGAAAACCTTCTCAGAAGCGA
TTATTTCCGGTGAGTGGAAAGGTTATACCGGCAAAGCAATCACTGACGTAGTGAACATCGGGATCGGCGGTTCTGACCTCGGCCCATACATGGTGACCGA
AGCTCTGCGTCCGTACAAAAACCACCTGAACATGCACTTTGTTTCTAACGTCGATGGGACTCACATCGCGGAAGTGCTGAAAAAAGTAAACCCGGAAACC
ACGCTGTTCTTGGTAGCATCTAAAACCTTCACCACTCAGGAAACTATGACCAACGCCCATAGCGCGCGTGACTGGTTCCTGAAAGCGGCAGGTGATGAAA
AACACGTTGCAAAACACTTTGCGGCGCTTTCCACCAATGCCAAAGCCGTTGGCGAGTTTGGTATTGATACTGCCAACATGTTCGAGTTCTGGGACTGGGT
TGGCGGCCGTTACTCTTTGTGGTCAGCGATTGGCCTGTCGATTGTTCTCTCCATCGGCTTTGATAACTTCGTTGAACTGCTTTCCGGCGCACACGCGATG
GACAAGCATTTCTCCACCACGCCTGCCGAGAAAAACCTGCCTGTACTGCTGGCGCTGATTGGCATCTGGTACAACAATTTCTTTGGTGCGGAAACTGAAG
CGATTCTGCCGTATGACCAGTATATGCACCGTTTCGCGGCGTACTTCCAGCAGGGCAATATGGAGTCCAACGGTAAGTATGTTGACCGTAACGGTAACGT
TGTGGATTACCAGACTGGCCCGATTATCTGGGGTGAACCAGGCACTAACGGTCAGCACGCGTTCTACCAGCTGATCCACCAGGGAACCAAAATGGTACCG
TGCGATTTCATCGCTCCGGCTATCACCCATAACCCGCTCTCTGATCATCACCAGAAACTGCTGTCTAACTTCTTCGCCCAGACCGAAGCGCTGGCGTTTG
GTAAATCCCGCGAAGTGGTTGAGCAGGAATATCGTGATCAGGGTAAAGATCCGGCAACGCTTGACTACGTGGTGCCGTTCAAAGTATTCGAAGGTAACCG
CCCGACCAACTCCATCCTGCTGCGTGAAATCACTCCGTTCAGCCTGGGTGCGTTGATTGCGCTGTATGAGCACAAAATCTTTACTCAGGGCGTGATCCTG
AACATCTTCACCTTCGACCAGTGGGGCGTGGAACTGGGTAAACAGCTGGCGAACCGTATTCTGCCAGAGCTGAAAGATGATAAAGAAATCAGCAGCCACG
ATAGCTCGACCAATGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAA

Loop counts:

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

Tetra-loop variants:

ACAC    2
UACA    1
UGGC    1

Single bulge variants:

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

1 x 1 internal loop variants:

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