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

ATGCAAGAGCAATACCGCCCGGAAGAGATAGAATCCAAAGTACAGCTTCATTGGGATGAGAAGCGCACATTTGAAGTAACCGAAGACGAGAGCAAAGAGA
AGTATTACTGCCTGTCTATGCTTCCCTATCCTTCTGGTCGACTACACATGGGCCACGTACGTAACTACACCATCGGTGACGTGATCGCCCGCTACCAGCG
TATGCTGGGCAAAAACGTCCTGCAGCCGATCGGCTGGGACGCGTTTGGTCTGCCTGCGGAAGGCGCGGCGGTGAAAAACAACACCGCTCCGGCACCGTGG
ACGTACGACAACATCGCGTATATGAAAAACCAGCTCAAAATGCTGGGCTTTGGTTATGACTGGAGCCGCGAGCTGGCAACCTGTACGCCGGAATACTACC
GTTGGGAACAGAAATTCTTCACCGAGCTGTATAAAAAAGGCCTGGTATATAAGAAGACTTCTGCGGTCAACTGGTGCCCGAACGACCAGACCGTACTGGC
GAACGAACAAGTTATCGACGGCTGCTGCTGGCGCTGCGATACCAAAGTTGAACGTAAAGAGATCCCGCAGTGGTTTATCAAAATCACTGCTTACGCTGAC
GAGCTGCTCAACGATCTGGATAAACTGGATCACTGGCCAGACACCGTTAAAACCATGCAGCGTAACTGGATCGGTCGTTCCGAAGGCGTGGAGATCACCT
TCAACGTTAACGACTATGACAACACGCTGACCGTTTACACTACCCGCCCGGACACCTTTATGGGTTGTACCTACCTGGCGGTAGCTGCGGGTCATCCGCT
GGCGCAGAAAGCGGCGGAAAATAATCCTGAACTGGCGGCCTTTATTGACGAATGCCGTAACACCAAAGTTGCCGAAGCTGAAATGGCGACGATGGAGAAA
AAAGGCGTCGATACTGGCTTTAAAGCGGTTCACCCATTAACGGGCGAAGAAATTCCCGTTTGGGCAGCAAACTTCGTATTGATGGAGTACGGCACGGGCG
CAGTTATGGCGGTACCGGGGCACGACCAGCGCGACTACGAGTTTGCCTCTAAATACGGCCTGAACATCAAACCGGTTATCCTGGCAGCTGACGGCTCTGA
GCCAGATCTTTCTCAGCAAGCCCTGACTGAAAAAGGCGTGCTGTTCAACTCTGGCGAGTTCAACGGTCTTGACCATGAAGCGGCCTTCAACGCCATCGCC
GATAAACTGACTGCGATGGGCGTTGGCGAGCGTAAAGTGAACTACCGCCTGCGCGACTGGGGTGTTTCCCGTCAGCGTTACTGGGGCGCGCCGATTCCGA
TGGTGACGCTGGAAGACGGTACCGTAATGCCGACCCCGGACGACCAGCTGCCGGTGATCCTGCCGGAAGATGTGGTAATGGACGGCATTACCAGCCCGAT
TAAAGCAGATCCGGAGTGGGCGAAAACTACCGTTAACGGTATGCCAGCACTGCGTGAAACCGACACTTTCGACACCTTTATGGAGTCCTCCTGGTACTAT
GCGCGCTACACTTGCCCGCAGTACAAAGAAGGTATGCTGGATTCCGAAGCGGCTAACTACTGGCTGCCGGTGGATATCTACATTGGTGGTATTGAACACG
CCATTATGCACCTGCTCTACTTCCGCTTCTTCCACAAACTGATGCGTGATGCAGGCATGGTGAACTCTGACGAACCAGCGAAACAGTTGCTGTGTCAGGG
TATGGTGCTGGCAGATGCCTTCTACTATGTTGGCGAAAACGGCGAACGTAACTGGGTTTCCCCGGTTGATGCTATCGTTGAACGTGACGAGAAAGGCCGT
ATCGTGAAAGCGAAAGATGCGGCAGGCCATGAACTGGTTTATACCGGCATGAGCAAAATGTCCAAGTCGAAGAACAACGGTATCGACCCGCAGGTGATGG
TTGAACGTTACGGCGCGGACACCGTTCGTCTGTTTATGATGTTTGCTTCTCCGGCTGATATGACTCTCGAATGGCAGGAATCCGGTGTGGAAGGGGCTAA
CCGCTTCCTGAAACGTGTCTGGAAACTGGTTTACGAGCACACAGCAAAAGGTGATGTTGCGGCACTGAACGTTGATGCGCTGACTGAAAATCAGAAAGCG
CTGCGTCGCGATGTGCATAAAACGATCGCTAAAGTGACCGATGATATCGGCCGTCGTCAGACCTTCAACACCGCAATTGCGGCGATTATGGAGCTGATGA
ACAAACTGGCGAAAGCACCAACCGATGGCGAGCAGGATCGCGCTCTGATGCAGGAAGCACTGCTGGCCGTTGTCCGTATGCTTAACCCGTTCACCCCGCA
CATCTGCTTCACGCTGTGGCAGGAACTGAAAGGCGAAGGCGATATCGACAACGCGCCGTGGCCGGTTGCTGACGAAAAAGCGATGGTGGAAGACTCCACG
CTGGTCGTGGTGCAGGTTAACGGTAAAGTCCGTGCCAAAATCACCGTTCCGGTGGACGCAACGGAAGAACAGGTTCGCGAACGTGCTGGCCAGGAACATC
TGGTAGCAAAATATCTTGATGGCGTTACTGTACGTAAAGTGATTTACGTACCAGGTAAACTCCTCAATCTGGTCGTTGGCTAA

Loop counts:

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

Tetra-loop variants:

UUAU    2
UGUU    1
UUUC    1
AAUU    1
GAUC    1
GUGA    1
UAUG    1
AUCA    1

Single bulge variants:

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

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