Annotated gene sequence

Experiment = in-cell 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

ATGAGTGACTATAAATCAACCCTGAATTTGCCGGAAACAGGGTTCCCGATGCGTGGCGATCTCGCCAAGCGCGAACCCGGAATGCTGGCGCGTTGGACTG
ATGATGATCTGTACGGCATCATCCGTGCGGCTAAAAAAGGCAAAAAAACCTTCATTCTGCATGATGGCCCTCCTTATGCGAATGGCAGCATTCATATTGG
TCACTCGGTTAACAAGATTCTGAAAGACATTATCGTGAAGTCCAAAGGGCTTTCCGGTTATGACTCGCCGTATGTGCCTGGCTGGGACTGCCACGGTCTG
CCGATCGAGCTGAAAGTCGAGCAAGAATACGGTAAGCCGGGTGAGAAATTCACCGCCGCCGAGTTCCGCGCCAAGTGCCGCGAATACGCGGCGACCCAGG
TTGACGGTCAACGCAAAGACTTTATCCGTCTGGGCGTGCTGGGCGACTGGTCGCACCCGTACCTGACCATGGACTTCAAAACTGAAGCCAACATCATCCG
CGCGCTGGGCAAAATCATCGGCAACGGTCACCTGCACAAAGGCGCGAAGCCAGTTCACTGGTGCGTTGACTGCCGTTCTGCGCTGGCGGAAGCGGAAGTT
GAGTATTACGACAAAACTTCTCCGTCCATCGACGTTGCTTTCCAGGCAGTCGATCAGGATGCACTGAAAGCAAAATTTGCCGTAAGCAACGTTAACGGCC
CAATCTCGCTGGTAATCTGGACCACCACGCCGTGGACTCTGCCTGCCAACCGCGCAATCTCTATTGCACCAGATTTCGACTATGCGCTGGTGCAGATCGA
CGGTCAGGCCGTGATTCTGGCGAAAGATCTGGTTGAAAGCGTAATGCAGCGTATCGGCGTGACCGATTACACCATTCTCGGCACGGTAAAAGGTGCGGAG
CTTGAGCTGCTGCGCTTTACCCATCCGTTTATGGGCTTCGACGTTCCGGCAATCCTCGGCGATCACGTTACCCTGGATGCCGGTACCGGTGCCGTTCACA
CCGCGCCTGGCCACGGCCCGGACGACTATGTGATCGGTCAGAAATACGGCCTGGAAACCGCTAACCCGGTTGGCCCGGACGGCACTTATCTGCCGGGCAC
TTATCCGACGCTGGATGGCGTGAACGTCTTCAAAGCGAACGACATCGTCGTTGCGCTGCTGCAGGAAAAAGGCGCGCTGCTGCACGTTGAGAAAATGCAG
CACAGCTATCCGTGCTGCTGGCGTCACAAAACGCCGATCATCTTCCGCGCGACGCCGCAGTGGTTCGTCAGCATGGATCAGAAAGGTCTGCGTGCGCAGT
CACTGAAAGAGATCAAAGGCGTGCAGTGGATCCCGGACTGGGGCCAGGCGCGTATCGAGTCGATGGTTGCTAACCGTCCTGACTGGTGTATCTCCCGTCA
GCGCACCTGGGGTGTACCGATGTCACTGTTCGTGCACAAAGACACGGAAGAGCTGCATCCGCGTACCCTTGAACTGATGGAAGAAGTGGCAAAACGCGTT
GAAGTCGATGGCATCCAGGCGTGGTGGGATCTCGATGCGAAAGAGATCCTCGGCGACGAAGCTGATCAGTACGTGAAAGTGCCGGACACATTGGATGTAT
GGTTTGACTCCGGATCTACCCACTCTTCTGTTGTTGACGTGCGTCCGGAATTTGCCGGTCACGCAGCGGACATGTATCTGGAAGGTTCTGACCAACACCG
CGGCTGGTTCATGTCTTCCCTAATGATCTCCACCGCGATGAAGGGTAAAGCGCCGTATCGTCAGGTACTGACCCACGGCTTTACCGTGGATGGTCAGGGC
CGCAAGATGTCTAAATCCATCGGCAATACCGTTTCGCCGCAGGATGTGATGAACAAACTGGGCGCGGATATTCTGCGTCTGTGGGTGGCATCAACCGACT
ACACCGGTGAAATGGCCGTTTCTGACGAGATCCTGAAACGTGCTGCCGATAGCTATCGTCGTATCCGTAACACCGCGCGCTTCCTGCTGGCAAACCTGAA
CGGTTTTGATCCAGCAAAAGATATGGTGAAACCGGAAGAGATGGTGGTACTGGATCGCTGGGCCGTAGGTTGTGCGAAAGCGGCACAGGAAGACATCCTC
AAGGCGTACGAAGCATACGATTTCCACGAAGTGGTACAGCGTCTGATGCGCTTCTGCTCCGTTGAGATGGGTTCCTTCTACCTCGACATCATCAAAGACC
GTCAGTACACCGCCAAAGCGGACAGTGTGGCGCGTCGTAGCTGCCAGACTGCGCTATATCACATCGCAGAAGCGCTGGTGCGCTGGATGGCACCAATCCT
CTCCTTCACCGCTGATGAAGTGTGGGGCTACCTGCCGGGCGAACGTGAAAAATACGTCTTCACCGGTGAGTGGTACGAAGGCCTGTTTGGCCTGGCAGAC
AGTGAAGCGATGAACGATGCGTTCTGGGACGAGCTGTTGAAAGTGCGTGGCGAAGTGAACAAAGTCATTGAGCAAGCGCGTGCCGACAAGAAAGTGGGTG
GCTCGCTGGAAGCGGCAGTAACCTTGTATGCAGAACCGGAACTGTCGGCGAAACTGACCGCGCTGGGCGATGAATTACGATTTGTCCTGTTGACCTCCGG
CGCTACCGTTGCAGACTATAACGACGCACCTGCTGATGCTCAGCAGAGCGAAGTACTCAAAGGGCTGAAAGTCGCGTTGAGTAAAGCCGAAGGTGAGAAG
TGCCCACGCTGCTGGCACTACACCCAGGATGTCGGCAAGGTGGCGGAACACGCAGAAATCTGCGGCCGCTGTGTCAGCAACGTCGCCGGTGACGGTGAAA
AACGTAAGTTTGCCTGA

Loop counts:

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

Tetra-loop variants:

CCCU    1
CAAA    1
GAAG    1
AAAU    1
AUCU    1

Single bulge variants:

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

1 x 1 bulge variants:

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