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 
ATGTCTGAAATGACCCCACGCGAAATCGTCAGCGAACTGGATAAGCACATCATCGGCCAGGACAACGCCAAGCGTTCTGTGGCGATTGCTCTGCGTAACC
GCTGGCGTCGCATGCAGCTCAACGAAGAGCTGCGCCATGAAGTGACCCCGAAAAATATCCTGATGATCGGCCCGACCGGTGTCGGTAAAACTGAAATCGC
CCGTCGTCTGGCTAAGCTGGCGAATGCGCCGTTCATCAAAGTTGAAGCGACCAAATTCACCGAAGTGGGCTACGTCGGTAAGGAAGTGGATTCTATTATT
CGCGATCTGACCGATGCCGCCGTGAAAATGGTACGCGTCCAGGCTATCGAGAAAAACCGTTATCGCGCTGAAGAACTGGCAGAAGAACGTATTCTCGACG
TGCTGATCCCACCTGCTAAAAACAACTGGGGACAGACCGAACAGCAGCAGGAACCGTCCGCTGCTCGTCAGGCATTCCGCAAAAAACTGCGTGAAGGCCA
GCTTGATGACAAAGAAATCGAGATCGATCTTGCCGCAGCACCGATGGGCGTTGAAATTATGGCTCCTCCGGGCATGGAAGAGATGACCAGCCAGCTGCAG
TCCATGTTCCAGAACCTGGGCGGCCAGAAGCAAAAAGCGCGTAAGCTGAAAATCAAAGACGCCATGAAGCTGCTGATTGAAGAAGAAGCGGCGAAACTGG
TGAACCCGGAAGAGCTGAAGCAAGACGCTATCGACGCTGTTGAGCAGCACGGGATCGTGTTTATCGACGAAATCGACAAAATCTGTAAGCGCGGCGAGTC
TTCCGGTCCGGATGTTTCTCGTGAAGGCGTTCAGCGTGACCTGCTGCCGCTGGTAGAAGGTTGCACCGTTTCCACCAAACACGGGATGGTCAAAACTGAC
CACATTCTGTTTATCGCTTCTGGCGCGTTCCAGATTGCGAAACCGTCTGACCTGATCCCGGAACTGCAAGGTCGTCTGCCAATCCGCGTTGAACTGCAGG
CGCTGACCACCAGCGACTTCGAGCGTATTCTGACCGAGCCGAATGCCTCTATCACCGTGCAGTACAAAGCACTGATGGCGACTGAAGGCGTAAATATCGA
GTTTACCGACTCCGGTATTAAACGCATCGCGGAAGCGGCATGGCAGGTGAACGAATCTACCGAAAACATCGGTGCTCGTCGTTTACACACTGTTCTGGAG
CGTTTAATGGAAGAGATTTCCTACGACGCCAGCGATTTAAGCGGTCAAAATATCACTATTGACGCAGATTATGTGAGCAAACATCTGGATGCGTTGGTGG
CAGATGAAGATCTGAGCCGTTTTATCCTATAA

Loop counts:

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

Tetra-loop variants:

UACC    1
CGGU    1
ACCG    1
GAAG    1
GGAU    1
AAAC    1

Single bulge variants:

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

1 x 1 bulge variants:

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