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

ATGACAGATGTAACGATTAAAACGCTGGCCGCAGAGCGACAGACCTCCGTGGAACGCCTGGTACAGCAATTTGCTGATGCAGGTATCCGGAAGTCTGCTG
ACGACTCTGTGTCTGCACAAGAGAAACAGACTTTGATTGACCACCTGAATCAGAAAAATTCAGGCCCGGACAAATTGACGCTGCAACGTAAAACACGCAG
CACCCTTAACATTCCTGGTACCGGTGGAAAAAGCAAATCGGTACAAATCGAAGTCCGCAAGAAACGCACCTTTGTGAAACGCGATCCGCAAGAGGCTGAA
CGCCTTGCAGCGGAAGAGCAAGCGCAGCGTGAAGCGGAAGAGCAAGCCCGTCGTGAGGCAGAAGAATCGGCTAAACGCGAGGCGCAACAAAAAGCTGAAC
GTGAGGCCGCAGAACAAGCTAAGCGTGAAGCTGCTGAACAAGCGAAACGTGAAGCTGCGGAAAAAGACAAAGTGAGCAATCAACAAGACGATATGACTAA
AAACGCCCAGGCTGAAAAAGCCCGCCGTGAGCAGGAAGCTGCAGAGCTCAAGCGTAAAGCTGAAGAAGAAGCGCGTCGTAAACTCGAAGAAGAAGCACGT
CGCGTTGCTGAAGAAGCACGTCGTATGGCGGAAGAAAACAAATGGACTGATAACGCGGAACCGACTGAAGATTCCAGCGATTATCACGTCACTACTTCTC
AACATGCTCGCCAGGCAGAAGACGAAAGCGATCGTGAAGTCGAAGGCGGCCGTGGCCGTGGTCGTAACGCGAAAGCAGCGCGTCCGAAGAAAGGCAACAA
ACACGCTGAATCAAAAGCTGATCGTGAAGAAGCACGCGCAGCAGTACGTGGCGGTAAAGGCGGAAAACGTAAAGGTTCTTCGCTGCAGCAAGGCTTCCAG
AAGCCTGCTCAGGCCGTTAACCGTGACGTTGTGATCGGCGAAACTATCACCGTTGGCGAACTGGCGAACAAGATGGCGGTTAAAGGCTCTCAGGTCATCA
AAGCGATGATGAAACTGGGCGCAATGGCAACCATCAACCAGGTTATCGATCAGGAAACCGCACAGCTGGTTGCTGAAGAGATGGGCCATAAAGTTATCCT
GCGTCGTGAAAACGAGCTGGAAGAGGCGGTAATGAGCGACCGTGACACGGGTGCTGCGGCTGAACCGCGCGCGCCGGTTGTGACCATCATGGGTCACGTT
GACCACGGTAAAACCTCTCTGCTGGACTACATTCGTTCAACGAAAGTGGCCTCTGGCGAAGCGGGCGGCATTACCCAGCACATTGGTGCATACCACGTTG
AAACTGAAAACGGCATGATCACCTTCCTGGACACCCCGGGGCACGCCGCGTTTACTTCAATGCGTGCTCGTGGTGCGCAGGCAACGGACATCGTAGTCCT
GGTTGTTGCTGCCGACGACGGTGTGATGCCGCAGACCATCGAAGCAATCCAGCACGCGAAAGCGGCGCAGGTACCGGTGGTGGTTGCAGTGAACAAGATC
GATAAACCAGAAGCTGATCCGGATCGCGTTAAGAACGAACTCTCCCAGTACGGCATCCTGCCGGAAGAGTGGGGCGGTGAAAGCCAGTTCGTACACGTAT
CTGCGAAAGCGGGTACCGGTATCGATGAACTGCTGGACGCTATCCTGCTGCAGGCGGAAGTTCTGGAGCTGAAAGCGGTACGTAAAGGTATGGCGAGCGG
TGCGGTTATCGAATCCTTCCTCGATAAAGGTCGTGGTCCGGTTGCTACCGTTCTGGTACGTGAAGGTACTCTGCACAAGGGCGATATCGTTCTGTGTGGC
TTCGAATACGGTCGTGTTCGTGCGATGCGTAACGAACTGGGTCAGGAAGTGCTGGAAGCGGGTCCGTCCATTCCGGTGGAAATCCTCGGCCTGTCCGGCG
TACCGGCTGCGGGTGATGAAGTTACCGTTGTACGTGACGAGAAGAAAGCGCGTGAAGTTGCACTCTATCGTCAGGGTAAATTCCGCGAAGTTAAACTGGC
GCGTCAGCAGAAATCTAAACTCGAGAACATGTTCGCCAACATGACCGAAGGCGAAGTTCACGAAGTGAATATCGTCCTGAAGGCAGACGTACAGGGTTCT
GTCGAAGCGATCTCCGACTCCTTGCTGAAACTGTCTACTGACGAAGTTAAAGTGAAGATCATCGGTTCTGGCGTAGGTGGTATCACCGAAACCGACGCCA
CCCTGGCTGCGGCGTCCAACGCCATCCTGGTTGGCTTTAACGTACGTGCTGATGCCTCTGCACGTAAAGTGATTGAAGCGGAAAGCCTGGATCTGCGTTA
CTACTCCGTCATCTATAACCTGATTGACGAAGTGAAAGCGGCGATGAGCGGTATGCTGTCTCCGGAACTGAAACAGCAGATTATCGGTCTGGCGGAAGTT
CGTGACGTGTTCAAATCGCCGAAATTTGGTGCCATCGCAGGCTGTATGGTTACCGAAGGTGTGGTTAAACGTCACAACCCGATCCGCGTTCTGCGTGACA
ACGTGGTTATCTACGAAGGCGAGCTGGAGTCCCTGCGCCGCTTCAAAGATGACGTTAACGAAGTCCGTAACGGTATGGAATGTGGTATCGGCGTTAAGAA
CTACAACGACGTCCGCACTGGCGATGTGATCGAAGTATTCGAAATCATCGAGATCCAACGTACCATTGCTTAA

Loop counts:

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

Tetra-loop variants:

GAAA    2
AUUG    1
AUAU    1
UCCG    1
CGUA    1
GUAU    1
CCAG    1

Single bulge variants:

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

1 x 1 internal loop variants:

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