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

ATGGCTCGTACAACACCCATCGCACGCTACCGTAACATCGGTATCAGTGCGCACATCGACGCCGGTAAAACCACTACTACCGAACGTATTCTGTTCTACA
CCGGTGTAAACCATAAAATCGGTGAAGTTCATGACGGCGCTGCAACCATGGACTGGATGGAGCAGGAGCAGGAACGTGGTATTACCATCACTTCCGCTGC
GACTACTGCATTCTGGTCTGGTATGGCTAAGCAGTATGAGCCGCATCGCATCAACATCATCGACACCCCGGGGCACGTTGACTTCACAATCGAAGTAGAA
CGTTCCATGCGTGTTCTCGATGGTGCGGTAATGGTTTACTGCGCAGTTGGTGGTGTTCAGCCGCAGTCTGAAACCGTATGGCGTCAGGCAAACAAATATA
AAGTTCCGCGCATTGCGTTCGTTAACAAAATGGACCGCATGGGTGCGAACTTCCTGAAAGTTGTTAACCAGATCAAAACCCGTCTGGGCGCGAACCCGGT
TCCGCTGCAGCTGGCGATTGGTGCTGAAGAACATTTCACCGGTGTTGTTGACCTGGTGAAAATGAAAGCTATCAACTGGAACGACGCTGACCAGGGCGTA
ACCTTCGAATACGAAGATATCCCGGCAGACATGGTTGAACTGGCTAACGAATGGCACCAGAACCTGATCGAATCCGCAGCTGAAGCTTCTGAAGAGCTGA
TGGAAAAATACCTGGGTGGTGAAGAACTGACTGAAGCAGAAATCAAAGGTGCTCTGCGTCAGCGCGTTCTGAACAACGAAATCATCCTGGTAACCTGTGG
TTCTGCGTTCAAGAACAAAGGTGTTCAGGCGATGCTGGATGCGGTAATTGATTACCTGCCATCCCCGGTTGACGTACCTGCGATCAACGGTATCCTGGAC
GACGGTAAAGACACTCCGGCTGAACGTCACGCAAGTGATGACGAGCCGTTCTCTGCACTGGCGTTCAAAATCGCTACCGACCCGTTTGTTGGTAACCTGA
CCTTCTTCCGTGTTTACTCCGGTGTGGTTAACTCTGGTGATACCGTACTGAACTCCGTGAAAGCTGCACGTGAGCGTTTCGGTCGTATCGTTCAGATGCA
CGCTAACAAACGTGAAGAGATCAAAGAAGTTCGCGCGGGCGACATCGCTGCTGCTATCGGTCTGAAAGACGTAACCACTGGTGACACCCTGTGTGACCCG
GATGCGCCGATCATTCTGGAACGTATGGAATTCCCTGAGCCGGTAATCTCCATCGCAGTTGAACCGAAAACCAAAGCTGACCAGGAAAAAATGGGTCTGG
CTCTGGGCCGTCTGGCTAAAGAAGACCCGTCTTTCCGTGTATGGACTGACGAAGAATCTAACCAGACCATCATCGCGGGTATGGGCGAACTGCACCTCGA
CATCATCGTTGACCGTATGAAGCGTGAATTCAACGTTGAAGCGAACGTAGGTAAACCGCAGGTTGCTTACCGTGAAACTATCCGCCAGAAAGTTACCGAT
GTTGAAGGTAAACACGCGAAACAGTCTGGTGGTCGTGGTCAGTATGGTCATGTTGTTATCGACATGTACCCGCTGGAGCCGGGTTCAAACCCGAAAGGCT
ACGAGTTCATCAACGACATTAAAGGTGGTGTAATCCCTGGCGAATACATCCCGGCCGTTGATAAAGGTATCCAGGAACAGCTGAAAGCAGGTCCGCTGGC
AGGCTACCCGGTAGTAGACATGGGTATTCGTCTGCACTTCGGTTCTTACCATGACGTTGACTCCTCTGAACTGGCGTTTAAACTGGCTGCTTCTATCGCC
TTTAAAGAAGGCTTTAAGAAAGCGAAACCAGTTCTGCTTGAGCCGATCATGAAGGTTGAAGTAGAAACTCCGGAAGAGAACACCGGTGACGTTATCGGTG
ACTTGAGCCGTCGTCGTGGTATGCTCAAAGGTCAGGAATCTGAAGTTACTGGCGTTAAGATCCACGCTGAAGTACCGCTGTCTGAAATGTTCGGATACGC
AACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCAGGCCGTAATTGAA
GCCCGTGGTAAATAA

Loop counts:

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

Tetra-loop variants:

GUCU    1
UUAU    1
UCAA    1
AAUU    1
ACGU    1
AAUA    1
UUGA    1
GCAA    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 3
U x 0 bulge: 4
C x 0 bulge: 1

1 x 1 bulge variants:

G x G bulge: 3
G x A bulge: 0
G x U bulge: 0
G x C bulge: 0
A x G bulge: 0
A x A bulge: 2
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