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

ATGGGTAAAGCTCTTGTCATCGTTGAGTCCCCGGCAAAAGCCAAAACGATCAACAAGTATCTGGGTAGTGACTACGTGGTGAAATCCAGCGTCGGTCACA
TCCGCGATTTGCCGACCAGTGGCTCAGCTGCCAAAAAGAGTGCCGACTCTACCTCCACCAAGACGGCTAAAAAGCCTAAAAAGGATGAACGTGGCGCTCT
CGTCAACCGTATGGGGGTTGACCCGTGGCACAATTGGGAGGCGCACTATGAAGTGTTGCCTGGTAAAGAGAAGGTCGTCTCTGAACTGAAACAACTGGCT
GAAAAAGCCGACCACATCTATCTCGCAACCGACCTTGACCGCGAAGGGGAAGCCATTGCATGGCACCTGCGGGAAGTGATTGGGGGTGATGATGCGCGCT
ATAGCCGAGTGGTGTTTAACGAAATTACTAAAAACGCGATCCGCCAGGCATTTAACAAACCGGGTGAGCTGAATATTGATCGTGTTAATGCCCAGCAGGC
GCGTCGCTTTATGGACCGCGTGGTGGGGTATATGGTTTCGCCGCTGCTATGGAAAAAGATCGCTCGTGGCCTGTCTGCCGGTCGTGTGCAGTCGGTGGCG
GTTCGCCTGGTGGTCGAGCGTGAGCGTGAAATTAAAGCGTTCGTGCCGGAAGAGTTCTGGGAAGTCGATGCCAGCACGACCACGCCATCTGGTGAAGCGT
TGGCGTTACAGGTGACTCATCAGAACGACAAACCGTTCCGTCCGGTCAACAAAGAACAAACTCAGGCTGCGGTAAGTCTGCTGGAAAAAGCGCGCTACAG
CGTGCTGGAACGTGAAGACAAACCGACAACCAGTAAACCTGGCGCTCCTTTTATTACCTCTACGCTGCAACAAGCTGCCAGCACCCGTCTTGGATTTGGC
GTGAAAAAAACCATGATGATGGCGCAGCGTTTGTATGAAGCAGGCTATATCACTTACATGCGTACCGACTCCACTAACCTGAGTCAGGACGCGGTAAATA
TGGTTCGCGGTTATATCAGCGATAATTTTGGTAAGAAATATCTGCCGGAAAGTCCGAATCAGTACGCCAGCAAAGAAAACTCACAGGAAGCGCACGAAGC
GATTCGTCCTTCTGACGTCAATGTGATGGCGGAATCGCTGAAGGATATGGAAGCAGATGCGCAGAAACTGTACCAGTTAATCTGGCGTCAGTTCGTTGCC
TGCCAGATGACCCCAGCGAAATATGACTCCACGACGCTGACCGTTGGTGCGGGCGATTTCCGCCTGAAAGCACGCGGTCGTATTTTGCGTTTTGATGGCT
GGACAAAAGTGATGCCTGCGTTGCGTAAAGGCGATGAAGATCGCATCTTACCAGCAGTTAATAAAGGCGATGCTCTGACGCTCGTTGAACTTACACCAGC
CCAGCACTTTACCAAGCCGCCAGCCCGTTTCAGTGAAGCATCGCTGGTTAAAGAGCTGGAAAAACGCGGTATCGGTCGTCCGTCTACCTATGCGTCGATC
ATTTCGACCATTCAGGATCGTGGCTACGTGCGAGTAGAAAATCGTCGTTTCTATGCGGAAAAAATGGGCGAAATCGTCACCGATCGCCTTGAAGAAAATT
TCCGCGAGTTAATGAACTACGACTTTACCGCGCAGATGGAAAACAGCCTCGACCAGGTGGCAAATCACGAAGCAGAGTGGAAAGCTGTACTGGATCACTT
CTTCTCGGATTTCACCCAGCAGTTAGATAAAGCTGAAAAAGATCCGGAAGAGGGTGGTATGCGCCCGAACCAGATGGTTCTGACCAGCATTGACTGCCCG
ACTTGTGGTCGCAAAATGGGGATTCGCACAGCGAGCACCGGGGTATTCCTTGGCTGTTCTGGCTATGCGCTGCCGCCGAAAGAGCGTTGCAAAACCACCA
TTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCAC
GGCGATGGACAGCTATCTCATCGATCCGAAACGTAAGTTGCATGTCTGTGGTAATAACCCAACCTGCGACGGTTACGAGATCGAAGAGGGCGAATTCCGC
ATTAAAGGTTATGACGGCCCGATCGTTGAGTGTGAAAAATGTGGCTCTGAAATGCACCTGAAAATGGGGCGTTTCGGTAAATACATGGCCTGCACCAACG
AAGAGTGTAAAAACACACGTAAGATTTTACGTAACGGCGAAGTGGCACCACCGAAAGAAGATCCGGTGCCATTACCTGAGCTGCCGTGCGAAAAATCAGA
TGCTTATTTCGTGCTGCGTGACGGTGCTGCCGGTGTGTTCCTGGCTGCCAACACTTTCCCGAAATCGCGTGAAACGCGTGCGCCACTGGTGGAAGAGCTT
TATCGCTTCCGCGACCGTCTGCCGGAAAAACTGCGTTATCTGGCCGATGCGCCACAGCAGGATCCGGAAGGTAATAAGACCATGGTTCGCTTTAGCCGTA
AAACCAAACAGCAATATGTCTCTTCGGAAAAAGACGGAAAGGCGACTGGCTGGTCAGCATTTTATGTTGATGGCAAATGGGTTGAAGGAAAAAAATAA

Loop counts:

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

Tetra-loop variants:

GAAG    1
UCAC    1
AAAA    1
AGAU    1
UAUU    1
AAUA    1
AUGA    1
UACA    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 7
U x 0 bulge: 2
C x 0 bulge: 5

1 x 1 internal loop 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: 3
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: 1
C x G bulge: 0
C x A bulge: 0
C x U bulge: 1
C x C bulge: 0