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

ATGAGCAAGAGCACCGCTGAGATCCGTCAGGCGTTTCTCGACTTTTTCCATAGTAAGGGACATCAGGTAGTTGCCAGCAGCTCCCTGGTACCCCATAACG
ACCCAACTTTGTTGTTTACCAACGCCGGGATGAACCAGTTCAAGGATGTGTTCCTTGGGCTCGACAAGCGTAATTATTCCCGCGCTACCACTTCCCAACG
CTGCGTGCGTGCGGGTGGTAAACACAACGACCTGGAAAACGTCGGTTACACCGCGCGTCACCATACCTTCTTCGAAATGCTGGGCAACTTCAGCTTCGGC
GACTATTTCAAACACGATGCCATTCAGTTTGCATGGGAACTGCTGACCAGCGAAAAATGGTTTGCCCTGCCGAAAGAGCGTCTGTGGGTTACCGTCTATG
AAAGCGACGACGAAGCCTACGAAATCTGGGAAAAAGAAGTAGGGATCCCGCGCGAACGTATTATTCGCATCGGCGATAACAAAGGTGCGCCATACGCATC
TGACAACTTCTGGCAGATGGGTGACACTGGTCCGTGCGGCCCGTGCACCGAAATCTTCTACGATCACGGCGACCACATTTGGGGGGGCCCTCCGGGAAGC
CCGGAAGAAGACGGCGACCGCTACATTGAGATCTGGAACATCGTCTTCATGCAGTTCAACCGCCAGGCCGATGGCACGATGGAACCGCTGCCGAAGCCGT
CTGTAGATACCGGTATGGGTCTGGAGCGTATTGCTGCGGTGCTGCAACACGTTAACTCTAACTATGACATCGACCTGTTCCGCACGCTGATCCAGGCGGT
AGCGAAAGTCACTGGCGCAACCGATCTGAGCAATAAATCGCTGCGCGTAATCGCTGACCACATTCGTTCTTGTGCGTTCCTGATCGCGGATGGCGTAATG
CCGTCCAATGAAAACCGTGGTTATGTACTGCGTCGTATCATTCGTCGCGCAGTGCGTCACGGTAATATGCTCGGCGCGAAAGAAACCTTCTTCTACAAAC
TGGTTGGTCCGCTGATCGACGTTATGGGCTCTGCGGGTGAAGACCTGAAACGCCAGCAGGCGCAGGTTGAGCAGGTGCTGAAGACTGAAGAAGAGCAGTT
TGCTCGTACTCTGGAGCGCGGTCTGGCGTTGCTGGATGAAGAGCTGGCAAAACTTTCTGGTGATACGCTGGATGGTGAAACTGCTTTCCGTCTGTACGAC
ACCTATGGCTTCCCGGTTGACCTGACGGCTGATGTTTGTCGTGAGCGCAACATCAAAGTTGACGAAGCTGGTTTTGAAGCTGCAATGGAAGAGCAGCGTC
GTCGCGCGCGCGAAGCCAGCGGCTTTGGTGCCGATTACAACGCAATGATCCGTGTTGACAGTGCATCTGAATTTAAAGGCTATGACCATCTGGAACTGAA
CGGCAAAGTGACTGCGCTGTTTGTTGATGGTAAAGCGGTTGATGCCATCAATGCAGGCCAGGAAGCTGTGGTCGTGCTGGATCAAACGCCATTCTATGCG
GAATCCGGCGGTCAGGTTGGCGATAAAGGCGAACTGAAAGGCGCTAACTTCTCCTTTGCGGTGGAAGATACGCAGAAATACGGCCAGGCGATTGGTCACA
TCGGTAAACTTGCTGCGGGTTCTCTGAAAGTGGGCGACGCGGTGCAGGCTGATGTTGATGAGGCTCGTCGCGCCCGTATTCGTCTGAATCACTCCGCAAC
GCACCTGATGCACGCTGCGCTGCGCCAGGTTCTGGGTACTCATGTATCGCAGAAAGGTTCACTGGTTAACGACAAGGTGCTGCGCTTCGACTTCTCACAC
AACGAAGCGATGAAACCAGAAGAGATTCGTGCGGTCGAAGACCTGGTGAACACACAGATTCGTCGCAATTTGCCGATCGAAACCAACATCATGGATCTCG
AAGCGGCGAAAGCGAAAGGTGCGATGGCGCTGTTCGGCGAGAAGTATGATGAGCGCGTACGCGTGCTGAGCATGGGCGATTTCTCTACCGAGTTGTGTGG
CGGTACTCACGCCAGCCGCACTGGTGATATTGGTCTGTTCCGCATCATCTCTGAATCGGGTACTGCTGCAGGCGTTCGTCGTATCGAAGCGGTAACCGGA
GAAGGTGCTATCGCCACCGTTCATGCAGACAGCGATCGCTTAAGCGAAGTCGCGCATCTGCTGAAAGGCGATAGCAATAATCTGGCTGATAAAGTGCGCT
CAGTACTGGAACGTACGCGTCAGCTGGAAAAAGAGTTACAACAGCTTAAAGAACAAGCTGCCGCACAGGAGAGCGCAAATCTTTCCAGTAAGGCAATTGA
TGTTAATGGTGTTAAGCTGTTGGTTAGCGAGCTTAGCGGTGTTGAGCCGAAAATGTTGCGTACCATGGTTGACGATTTAAAAAATCAGCTGGGGTCGACA
ATTATCGTGCTGGCAACGGTAGTCGAAGGTAAGGTTTCTCTGATTGCAGGCGTATCTAAGGACGTCACAGATCGTGTGAAAGCAGGGGAACTGATTGGTA
TGGTCGCTCAGCAGGTGGGCGGCAAGGGTGGTGGACGTCCTGACATGGCGCAAGCCGGTGGTACGGATGCTGCGGCCTTACCTGCAGCGTTAGCCAGTGT
GAAAGGCTGGGTCAGCGCGAAATTGCAATAA

Loop counts:

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

Tetra-loop variants:

CGCU    1
AGCA    1
UCAU    1
CAAC    1
CCAG    1

Single bulge variants:

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

1 x 1 bulge variants:

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