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

ATGCTAGTTGTAGAACTCATCATAGTTTTGCTGGCGATCTTCTTGGGCGCCAGATTGGGGGGAATAGGTATTGGTTTTGCAGGCGGATTGGGGGTGCTGG
TTCTTGCCGCTATTGGCGTTAAACCCGGTAACATCCCGTTCGATGTCATCTCCATTATCATGGCGGTTATCGCCGCTATTTCTGCCATGCAGGTTGCTGG
CGGTCTGGACTATCTGGTTCATCAGACAGAAAAGCTGCTGCGCCGTAACCCGAAATACATCACGATCCTCGCACCGATCGTGACCTATTTCCTGACTATC
TTTGCTGGTACTGGCAACATCTCTCTGGCGACACTGCCAGTTATCGCTGAAGTTGCGAAGGAACAAGGCGTTAAACCTTGCCGTCCGCTGTCTACTGCAG
TGGTATCCGCGCAGATTGCGATCACCGCATCGCCAATCTCAGCGGCAGTGGTTTACATGTCTTCCGTGATGGAAGGTCATGGCATCAGCTACCTCCATCT
GCTCTCCGTGGTCATCCCGTCCACCCTGCTGGCGGTTCTGGTGATGTCCTTCCTGGTCACTATGCTGTTCAACTCCAAACTCTCTGACGATCCGATTTAT
CGCAAGCGTCTGGAAGAGGGCCTGGTTGAACTGCGCGGTGAAAAGCAGATTGAAATCAAATCCGGTGCAAAAACGTCCGTCTGGCTGTTCCTGCTGGGCG
TAGTTGGCGTGGTTATCTATGCAATCATCAACAGCCCAAGCATGGGTCTGGTTGAAAAACCGCTGATGAACACCACCAACGCAATCCTGATCATCATGCT
CAGCGTTGCAACTCTGACCACCGTTATCTGTAAAGTCGATACCGACAACATCCTCAACTCCAGCACCTTCAAAGCAGGTATGAGCGCCTGTATTTGTATC
CTGGGTGTTGCGTGGCTGGGCGATACTTTCGTTTCCAACAACATCGACTGGATCAAAGATACCGCTGGTGAAGTGATTCAGGGTCATCCGTGGCTGCTGG
CCGTCATCTTCTTCTTTGCTTCTGCTCTGCTGTACTCTCAGGCTGCAACCGCAAAAGCACTGATGCCGATGGCTCTGGCACTGAACGTTTCACCGCTGAC
CGCTGTTGCTTCTTTCGCTGCGGTGTCTGGTCTGTTCATTCTGCCGACCTACCCGACGCTGGTTGCTGCGGTACAGATGGATGACACGGGTACTACCCGT
ATCGGTAAATTCGTCTTCAACCATCCGTTCTTCATCCCGGGTACTCTGGGTGTTGCCCTGGCCGTTTGCTTCGGCTTCGTGCTGGGTAGCTTCATGCTGT
AA

Loop counts:

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

Tetra-loop variants:

UAUC    1
UUUA    1

Single bulge variants:

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

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