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

GTGCTAGAAGAATACCGTAAGCACGTAGCTGAGCGTGCCGCTGAGGGGATTGCGCCCAAACCCCTGGATGCAAACCAAATGGCCGCACTTGTAGAGCTGC
TGAAAAACCCGCCCGCGGGCGAAGAAGAATTCCTGTTAGATCTGTTAACCAACCGTGTTCCCCCAGGCGTCGATGAAGCCGCCTATGTCAAAGCAGGCTT
CCTGGCTGCTATCGCGAAAGGCGAAGCCAAATCCCCTCTGCTGACTCCGGAAAAAGCCATCGAACTGCTGGGCACCATGCAGGGTGGTTACAACATTCAT
CCGCTGATCGACGCGCTGGATGATGCCAAACTGGCACCTATTGCTGCCAAAGCACTTTCTCACACGCTGCTGATGTTCGATAACTTCTATGACGTAGAAG
AGAAAGCGAAAGCAGGCAACGAATATGCGAAGCAGGTTATGCAGTCCTGGGCGGATGCCGAATGGTTCCTGAATCGCCCGGCGCTGGCTGAAAAACTGAC
CGTTACTGTCTTCAAAGTCACTGGCGAAACTAACACCGATGACCTTTCTCCGGCACCGGATGCGTGGTCACGCCCGGATATCCCACTGCACGCGCTGGCG
ATGCTGAAAAACGCCCGTGAAGGTATTGAGCCAGACCAGCCTGGTGTTGTTGGTCCGATCAAGCAAATCGAAGCTCTGCAACAGAAAGGTTTCCCGCTGG
CGTACGTCGGTGACGTTGTGGGTACGGGTTCTTCGCGTAAATCCGCCACTAACTCCGTTCTGTGGTTTATGGGCGATGATATTCCACATGTGCCGAACAA
ACGCGGCGGTGGTTTGTGCCTCGGCGGTAAAATTGCACCCATCTTCTTTAACACGATGGAAGACGCGGGTGCACTGCCAATCGAAGTCGACGTCTCTAAC
CTGAACATGGGCGACGTGATTGACGTTTACCCGTACAAAGGTGAAGTGCGTAACCACGAAACCGGCGAACTGCTGGCGACCTTCGAACTGAAAACCGACG
TGCTGATTGATGAAGTGCGTGCTGGTGGCCGTATTCCGCTGATTATCGGGCGTGGCCTGACCACCAAAGCGCGTGAAGCACTTGGTCTGCCGCACAGTGA
TGTGTTCCGTCAGGCGAAAGATGTCGCTGAGAGCGATCGCGGCTTCTCGCTGGCGCAAAAAATGGTAGGCCGTGCCTGTGGCGTGAAAGGCATTCGTCCG
GGCGCGTACTGTGAACCGAAAATGACTTCTGTAGGTTCCCAGGACACCACCGGCCCGATGACCCGTGATGAACTGAAAGACCTGGCGTGCCTGGGCTTCT
CGGCTGACCTGGTGATGCAGTCTTTCTGCCACACCGCGGCGTATCCGAAGCCAGTTGACGTGAACACGCACCACACGCTGCCGGACTTCATTATGAACCG
TGGCGGTGTGTCGCTGCGTCCGGGTGACGGCGTCATTCACTCCTGGCTGAACCGTATGCTGCTGCCGGATACCGTCGGTACCGGTGGTGACTCCCATACC
CGTTTCCCGATCGGTATCTCTTTCCCGGCGGGTTCTGGTCTGGTGGCGTTTGCTGCCGCAACTGGCGTAATGCCGCTTGATATGCCGGAATCCGTTCTGG
TGCGCTTCAAAGGCAAAATGCAGCCGGGCATCACCCTGCGCGATCTGGTACACGCTATTCCGCTGTATGCGATCAAACAAGGTCTGCTGACCGTTGAGAA
GAAAGGCAAGAAAAACATCTTCTCTGGCCGCATCCTGGAAATTGAAGGTCTGCCGGATCTGAAAGTTGAGCAGGCCTTTGAGCTAACCGATGCGTCCGCC
GAGCGTTCTGCCGCTGGTTGTACCATCAAGCTGAACAAAGAACCGATCATCGAATACCTGAACTCTAACATCGTCCTGCTGAAGTGGATGATCGCGGAAG
GTTACGGCGATCGTCGTACCCTGGAACGTCGTATTCAGGGCATGGAAAAATGGCTGGCGAATCCTGAGCTGCTGGAAGCCGATGCAGATGCGGAATACGC
GGCAGTGATCGACATCGATCTGGCGGATATTAAAGAGCCAATCCTGTGTGCTCCGAACGACCCGGATGACGCGCGTCCGCTGTCTGCGGTACAGGGTGAG
AAGATCGACGAAGTGTTTATCGGTTCCTGCATGACCAACATCGGTCACTTCCGTGCTGCGGGTAAACTGCTGGATGCGCATAAAGGTCAGTTGCCGACCC
GCCTGTGGGTGGCACCGCCAACCCGTATGGACGCCGCACAGTTGACCGAAGAAGGCTACTACAGCGTCTTCGGTAAGAGTGGTGCGCGTATCGAGATCCC
TGGCTGTTCCCTGTGTATGGGTAACCAGGCGCGTGTGGCGGACGGTGCAACGGTGGTTTCCACCTCTACCCGTAACTTCCCGAACCGTCTGGGTACTGGC
GCGAATGTCTTCCTGGCTTCTGCGGAACTGGCGGCTGTTGCGGCGCTGATTGGCAAACTGCCGACGCCGGAAGAGTACCAGACCTACGTGGCGCAGGTAG
ATAAAACAGCCGTTGATACTTACCGTTATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAA

Loop counts:

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

Tetra-loop variants:

GUGA    1
UGCU    1
GAUC    1
UUCU    1

Single bulge variants:

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

1 x 1 internal loop variants:

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