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
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: 9
5 nts: 3
6 nts: 6
7 nts: 2
9 nts: 1
10 nts: 1
Tetra-loop variants:
GUCU 1
UUAU 1
UCAA 1
ACGU 1
AAUU 1
GUAU 1
AAUA 1
UUGA 1
GCAA 1
Single bulge variants:
G x 0 bulge: 2
A x 0 bulge: 5
U x 0 bulge: 6
C x 0 bulge: 7
1 x 1 internal loop variants:
G x G bulge: 4
G x A bulge: 2
G x U bulge: 0
G x C bulge: 0
A x G bulge: 2
A x A bulge: 3
A x U bulge: 0
A x C bulge: 2
U x G bulge: 0
U x A bulge: 0
U x U bulge: 2
U x C bulge: 2
C x G bulge: 0
C x A bulge: 2
C x U bulge: 2
C x C bulge: 1