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

ATGAAATTACCGATTTATCTCGACTACTCCGCAACCACGCCGGTGGACCCGCGTGTTGCCGAGAAAATGATGCAGTTTATGACGATGGACGGAACCTTTG
GTAACCCGGCCTCCCGTTCTCACCGTTTCGGCTGGCAGGCTGAAGAAGCGGTAGATATCGCCCGTAATCAGATTGCCGATCTGGTCGGCGCTGATCCGCG
TGAAATCGTCTTTACCTCTGGTGCAACCGAATCTGACAACCTGGCGATCAAAGGTGCAGCCAACTTTTATCAGAAAAAAGGCAAGCACATCATCACCAGC
AAAACCGAACACAAAGCGGTACTGGATACCTGCCGTCAGCTGGAGCGCGAAGGTTTTGAAGTCACCTACCTGGCACCGCAGCGTAACGGCATTATCGACC
TGAAAGAACTTGAAGCAGCGATGCGTGACGACACCATCCTCGTGTCCATCATGCACGTAAATAACGAAATCGGCGTGGTGCAGGATATCGCGGCTATCGG
CGAAATGTGCCGTGCTCGTGGCATTATCTATCACGTTGATGCAACCCAGAGCGTGGGTAAACTGCCTATCGACCTGAGCCAGTTGAAAGTTGACCTGATG
TCTTTCTCCGGTCACAAAATCTATGGCCCGAAAGGTATCGGTGCGCTGTATGTACGTCGTAAACCGCGCGTACGCATCGAAGCGCAAATGCACGGCGGCG
GTCACGAGCGCGGTATGCGTTCCGGCACTCTGCCTGTTCACCAGATCGTCGGAATGGGCGAGGCCTATCGCATCGCAAAAGAAGAGATGGCGACCGAGAT
GGAACGTCTGCGCGGCCTGCGTAACCGTCTGTGGAACGGCATCAAAGATATCGAAGAAGTTTACCTGAACGGTGACCTGGAACACGGTGCGCCGAACATT
CTCAACGTCAGCTTCAACTACGTTGAAGGTGAGTCGCTGATTATGGCGCTGAAAGACCTCGCAGTTTCTTCAGGTTCCGCCTGTACGTCAGCAAGCCTCG
AACCGTCCTACGTGCTGCGCGCGCTGGGGCTGAACGACGAGCTGGCACATAGCTCTATCCGTTTCTCTTTAGGTCGTTTTACTACTGAAGAAGAGATCGA
CTACACCATCGAGTTAGTTCGTAAATCCATCGGTCGTCTGCGTGACCTTTCTCCGCTGTGGGAAATGTACAAGCAGGGCGTGGATCTGAACAGCATCGAA
TGGGCTCATCATTAA

Loop counts:

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

Tetra-loop variants:

GGCA    1
AUCA    1

Single bulge variants:

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