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

ATGAGCAAGAGCACCGCTGAGATCCGTCAGGCGTTTCTCGACTTTTTCCATAGTAAGGGACATCAGGTAGTTGCCAGCAGCTCCCTGGTACCCCATAACG
ACCCAACTTTGTTGTTTACCAACGCCGGGATGAACCAGTTCAAGGATGTGTTCCTTGGGCTCGACAAGCGTAATTATTCCCGCGCTACCACTTCCCAACG
CTGCGTGCGTGCGGGTGGTAAACACAACGACCTGGAAAACGTCGGTTACACCGCGCGTCACCATACCTTCTTCGAAATGCTGGGCAACTTCAGCTTCGGC
GACTATTTCAAACACGATGCCATTCAGTTTGCATGGGAACTGCTGACCAGCGAAAAATGGTTTGCCCTGCCGAAAGAGCGTCTGTGGGTTACCGTCTATG
AAAGCGACGACGAAGCCTACGAAATCTGGGAAAAAGAAGTAGGGATCCCGCGCGAACGTATTATTCGCATCGGCGATAACAAAGGTGCGCCATACGCATC
TGACAACTTCTGGCAGATGGGTGACACTGGTCCGTGCGGCCCGTGCACCGAAATCTTCTACGATCACGGCGACCACATTTGGGGGGGCCCTCCGGGAAGC
CCGGAAGAAGACGGCGACCGCTACATTGAGATCTGGAACATCGTCTTCATGCAGTTCAACCGCCAGGCCGATGGCACGATGGAACCGCTGCCGAAGCCGT
CTGTAGATACCGGTATGGGTCTGGAGCGTATTGCTGCGGTGCTGCAACACGTTAACTCTAACTATGACATCGACCTGTTCCGCACGCTGATCCAGGCGGT
AGCGAAAGTCACTGGCGCAACCGATCTGAGCAATAAATCGCTGCGCGTAATCGCTGACCACATTCGTTCTTGTGCGTTCCTGATCGCGGATGGCGTAATG
CCGTCCAATGAAAACCGTGGTTATGTACTGCGTCGTATCATTCGTCGCGCAGTGCGTCACGGTAATATGCTCGGCGCGAAAGAAACCTTCTTCTACAAAC
TGGTTGGTCCGCTGATCGACGTTATGGGCTCTGCGGGTGAAGACCTGAAACGCCAGCAGGCGCAGGTTGAGCAGGTGCTGAAGACTGAAGAAGAGCAGTT
TGCTCGTACTCTGGAGCGCGGTCTGGCGTTGCTGGATGAAGAGCTGGCAAAACTTTCTGGTGATACGCTGGATGGTGAAACTGCTTTCCGTCTGTACGAC
ACCTATGGCTTCCCGGTTGACCTGACGGCTGATGTTTGTCGTGAGCGCAACATCAAAGTTGACGAAGCTGGTTTTGAAGCTGCAATGGAAGAGCAGCGTC
GTCGCGCGCGCGAAGCCAGCGGCTTTGGTGCCGATTACAACGCAATGATCCGTGTTGACAGTGCATCTGAATTTAAAGGCTATGACCATCTGGAACTGAA
CGGCAAAGTGACTGCGCTGTTTGTTGATGGTAAAGCGGTTGATGCCATCAATGCAGGCCAGGAAGCTGTGGTCGTGCTGGATCAAACGCCATTCTATGCG
GAATCCGGCGGTCAGGTTGGCGATAAAGGCGAACTGAAAGGCGCTAACTTCTCCTTTGCGGTGGAAGATACGCAGAAATACGGCCAGGCGATTGGTCACA
TCGGTAAACTTGCTGCGGGTTCTCTGAAAGTGGGCGACGCGGTGCAGGCTGATGTTGATGAGGCTCGTCGCGCCCGTATTCGTCTGAATCACTCCGCAAC
GCACCTGATGCACGCTGCGCTGCGCCAGGTTCTGGGTACTCATGTATCGCAGAAAGGTTCACTGGTTAACGACAAGGTGCTGCGCTTCGACTTCTCACAC
AACGAAGCGATGAAACCAGAAGAGATTCGTGCGGTCGAAGACCTGGTGAACACACAGATTCGTCGCAATTTGCCGATCGAAACCAACATCATGGATCTCG
AAGCGGCGAAAGCGAAAGGTGCGATGGCGCTGTTCGGCGAGAAGTATGATGAGCGCGTACGCGTGCTGAGCATGGGCGATTTCTCTACCGAGTTGTGTGG
CGGTACTCACGCCAGCCGCACTGGTGATATTGGTCTGTTCCGCATCATCTCTGAATCGGGTACTGCTGCAGGCGTTCGTCGTATCGAAGCGGTAACCGGA
GAAGGTGCTATCGCCACCGTTCATGCAGACAGCGATCGCTTAAGCGAAGTCGCGCATCTGCTGAAAGGCGATAGCAATAATCTGGCTGATAAAGTGCGCT
CAGTACTGGAACGTACGCGTCAGCTGGAAAAAGAGTTACAACAGCTTAAAGAACAAGCTGCCGCACAGGAGAGCGCAAATCTTTCCAGTAAGGCAATTGA
TGTTAATGGTGTTAAGCTGTTGGTTAGCGAGCTTAGCGGTGTTGAGCCGAAAATGTTGCGTACCATGGTTGACGATTTAAAAAATCAGCTGGGGTCGACA
ATTATCGTGCTGGCAACGGTAGTCGAAGGTAAGGTTTCTCTGATTGCAGGCGTATCTAAGGACGTCACAGATCGTGTGAAAGCAGGGGAACTGATTGGTA
TGGTCGCTCAGCAGGTGGGCGGCAAGGGTGGTGGACGTCCTGACATGGCGCAAGCCGGTGGTACGGATGCTGCGGCCTTACCTGCAGCGTTAGCCAGTGT
GAAAGGCTGGGTCAGCGCGAAATTGCAATAA

Loop counts:

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

Tetra-loop variants:

AGCA    1
GCGC    1
UCAU    1
GAGA    1
UUAA    1
AUCG    1
GUGC    1
CCAG    1

Single bulge variants:

G x 0 bulge: 2
A x 0 bulge: 2
U x 0 bulge: 6
C x 0 bulge: 2

1 x 1 internal loop variants:

G x G bulge: 1
G x A bulge: 2
G x U bulge: 0
G x C bulge: 0
A x G bulge: 2
A x A bulge: 1
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: 3
C x G bulge: 0
C x A bulge: 0
C x U bulge: 3
C x C bulge: 0