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

ATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAG
ATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCT
GGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATG
TACATGCGTGAAATGGGCACCGTTGAACTGTTGACCCGCGAAGGCGAAATTGACATCGCTAAGCGTATTGAAGACGGGATCAACCAGGTTCAATGCTCCG
TTGCTGAATATCCGGAAGCGATCACCTATCTGCTGGAACAGTACGATCGTGTTGAAGCAGAAGAAGCGCGTCTGTCCGATCTGATCACCGGCTTTGTTGA
CCCGAACGCAGAAGAAGATCTGGCACCTACCGCCACTCACGTCGGTTCTGAGCTTTCCCAGGAAGATCTGGACGATGACGAAGATGAAGACGAAGAAGAT
GGCGATGACGACAGCGCCGATGATGACAACAGCATCGACCCGGAACTGGCTCGCGAAAAATTTGCGGAACTACGCGCTCAGTACGTTGTAACGCGTGACA
CCATCAAAGCGAAAGGTCGCAGTCACGCTACCGCTCAGGAAGAGATCCTGAAACTGTCTGAAGTATTCAAACAGTTCCGCCTGGTGCCGAAGCAGTTTGA
CTACCTGGTCAACAGCATGCGCGTCATGATGGACCGCGTTCGTACGCAAGAACGTCTGATCATGAAGCTCTGCGTTGAGCAGTGCAAAATGCCGAAGAAA
AACTTCATTACCCTGTTTACCGGCAACGAAACCAGCGATACCTGGTTCAACGCGGCAATTGCGATGAACAAGCCGTGGTCGGAAAAACTGCACGATGTCT
CTGAAGAAGTGCATCGCGCCCTGCAAAAACTGCAGCAGATTGAAGAAGAAACCGGCCTGACCATCGAGCAGGTTAAAGATATCAACCGTCGTATGTCCAT
CGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAG
TTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGT
GGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTC
TCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATC
GCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATT
CTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATAT
GAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCAC
CCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAA

Loop counts:

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

Tetra-loop variants:

GAAA    1
GCAA    1
GUAC    1
CCCG    1

Single bulge variants:

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

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