Annotated gene sequence

Experiment = cell-free 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

ATGAAAACGCTGCTGATTATTGACGCTAATCTCGGTCAGGCACGCGCCTATATGGCGAAGACCCTGCTGGGCGCGGCGGCGCGAAAAGCAAAACTGGAAA
TCATCGACAATCCGAACGACGCTGAAATGGCGATTGTTCTCGGTGATTCCATCCCGAACGACAGCGCGCTGAACGGTAAAAATGTCTGGCTGGGCGATAT
TTCCCGGGCAGTTGCGCACCCTGAGCTGTTCCTGAGTGAAGCCAAAGGCCATGCGAAACCTTACACTGCGCCGGTCGCTGCGACAGCACCAGTTGCCGCC
AGCGGTCCGAAACGCGTAGTTGCGGTGACTGCTTGCCCGACTGGCGTAGCACACACCTTTATGGCGGCTGAAGCCATTGAAACCGAAGCGAAAAAACGTG
GCTGGTGGGTGAAAGTTGAAACCCGTGGTTCTGTTGGCGCGGGTAATGCAATCACTCCCGAAGAAGTCGCAGCAGCGGATCTGGTGATTGTGGCGGCAGA
TATCGAAGTGGATCTGGCGAAATTTGCTGGTAAACCGATGTATCGTACCTCTACCGGTCTGGCGCTGAAGAAAACCGCGCAGGAACTGGATAAAGCGGTT
GCTGAAGCAACGCCGTATGAACCGGCGGGCAAAGCTCAAACGGCGACCACTGAAAGTAAGAAAGAGAGTGCAGGCGCATACCGTCACTTGCTGACGGGCG
TTTCTTACATGCTGCCGATGGTCGTTGCAGGTGGTCTGTGTATCGCGCTTTCTTTTGCTTTTGGTATCGAAGCGTTTAAAGAGCCGGGTACGTTGGCTGC
GGCGCTGATGCAGATTGGTGGTGGTTCAGCCTTTGCGCTGATGGTGCCGGTACTGGCAGGTTATATTGCCTTTTCCATTGCCGATCGTCCGGGCCTCACT
CCGGGTCTGATTGGCGGTATGCTGGCGGTCAGCACCGGTTCTGGCTTCATTGGTGGTATTATTGCGGGCTTCCTGGCTGGTTACATTGCGAAGTTAATCA
GTACGCAATTGAAACTGCCACAGAGTATGGAGGCGCTGAAACCGATCCTGATCATTCCGCTAATTTCCAGTCTGGTGGTCGGTCTGGCGATGATCTACCT
GATCGGTAAACCAGTTGCTGGCATTCTCGAAGGGCTGACTCACTGGCTGCAGACCATGGGGACTGCGAATGCGGTTCTGCTGGGGGCGATCCTCGGTGGC
ATGATGTGTACTGACATGGGCGGTCCGGTAAACAAAGCAGCGTACGCATTCGGTGTGGGTCTGCTGAGTACTCAAACCTATGGCCCGATGGCGGCGATTA
TGGCGGCAGGTATGGTGCCACCGCTGGCAATGGGTCTGGCAACAATGGTGGCGCGTCGCAAATTCGACAAAGCGCAGCAGGAAGGTGGCAAAGCCGCTCT
GGTATTGGGACTGTGCTTCATTTCGGAAGGTGCAATTCCGTTTGCTGCTCGTGATCCGATGCGTGTGCTGCCGTGCTGTATCGTGGGTGGGGCGCTGACT
GGCGCAATCTCAATGGCGATTGGTGCGAAACTGATGGCACCGCACGGTGGTCTGTTTGTTCTGCTGATCCCTGGCGCTATTACGCCGGTATTGGGTTACC
TGGTAGCAATTATTGCCGGTACGCTGGTGGCGGGTTTGGCCTATGCCTTCCTGAAACGTCCGGAAGTGGACGCAGTAGCGAAAGCAGCGTAA

Loop counts:

3 nts: 1
4 nts: 6
5 nts: 4
6 nts: 3
7 nts: 1
10 nts: 1

Tetra-loop variants:

GAAU    1
GCUG    1
GACU    1
GGCU    1
ACCA    1
GCGG    1

Single bulge variants:

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

1 x 1 internal loop 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: 1
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