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

ATGTTAGATATAGTCGAACTGTCGCGCTTACAGTTTGCCTTGACCGCGATGTACCACTTCCTTTTTGTGCCACTGACGCTCGGTATGGCGTTCCTGCTGG
CCATTATGGAAACGGTCTACGTCCTCTCCGGCAAACAGATTTATAAAGATATGACCAAGTTCTGGGGCAAGTTGTTTGGTATCAACTTCGCTCTGGGTGT
GGCTACCGGTCTGACCATGGAGTTCCAGTTCGGGACTAACTGGTCTTACTATTCCCACTATGTAGGGGATATCTTCGGTGCGCCGCTGGCAATCGAAGGT
CTGATGGCCTTCTTCCTCGAATCCACCTTTGTAGGTCTGTTCTTCTTCGGTTGGGATCGTCTGGGTAAAGTTCAGCATATGTGTGTCACCTGGCTGGTGG
CGCTCGGTTCAAACCTGTCCGCACTGTGGATTCTGGTTGCGAACGGCTGGATGCAAAACCCAATCGCGTCCGATTTCAACTTTGAAACTATGCGTATGGA
GATGGTGAGCTTCTCCGAGCTGGTGCTTAACCCGGTTGCTCAGGTGAAATTCGTTCACACTGTAGCGTCTGGTTATGTGACTGGCGCGATGTTCATCCTC
GGTATCAGCGCATGGTATATGCTGAAAGGTCGTGACTTCGCCTTCGCTAAACGCTCCTTTGCTATCGCTGCCAGCTTCGGTATGGCTGCTGTTCTGTCTG
TTATTGTTCTGGGTGATGAATCCGGCTACGAAATGGGCGACGTGCAGAAAACCAAACTGGCTGCTATTGAAGCCGAGTGGGAAACGCAACCTGCGCCTGC
TGCCTTTACTCTGTTCGGCATTCCTGATCAGGAAGAGGAGACGAACAAATTTGCGATTCAGATCCCTTACGCACTGGGCATCATTGCAACGCGTTCCGTG
GATACCCCGGTTATCGGCCTGAAAGAGCTGATGGTGCAGCATGAAGAACGCATTCGTAACGGGATGAAGGCGTACTCTCTGCTCGAACAACTGCGTTCTG
GTTCTACCGACCAGGCGGTTCGTGACCAGTTCAATAGCATGAAGAAAGACCTCGGTTACGGTCTGCTGCTGAAACGCTATACGCCAAACGTGGCTGATGC
GACTGAAGCGCAGATTCAACAGGCAACCAAAGACTCCATCCCGCGTGTAGCGCCGCTGTACTTTGCGTTCCGTATCATGGTGGCGTGTGGCTTCCTGCTT
CTGGCAATCATCGCGCTCTCTTTCTGGAGTGTCATCCGCAACCGCATTGGCGAGAAAAAATGGCTTCTGCGCGCCGCGCTGTACGGTATTCCGCTGCCGT
GGATTGCTGTAGAAGCGGGCTGGTTCGTGGCTGAATATGGCCGCCAACCGTGGGCTATCGGTGAAGTGCTGCCGACAGCTGTGGCGAACTCGTCACTGAC
CGCAGGCGATCTCATCTTCTCAATGGTGCTGATTTGCGGCCTGTATACCCTGTTCCTGGTGGCAGAATTGTTCTTAATGTTCAAGTTTGCACGCCTCGGC
CCAAGCAGCCTGAAAACCGGTCGCTATCACTTTGAGCAGTCTTCCACGACTACTCAGCCGGCACGCTAA

Loop counts:

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

Tetra-loop variants:

AACG    1
UGCC    1
AACU    1
UGAU    1
GAUC    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 2
U x 0 bulge: 3
C x 0 bulge: 4

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