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

GTGAAAGATTTATTAAAGTTTCTGAAAGCGCAGACTAAAACCGAAGAGTTTGATGCGATCAAAATTGCTCTGGCTTCGCCAGACATGATCCGTTCATGGT
CTTTCGGTGAAGTTAAAAAGCCGGAAACCATCAACTACCGTACGTTCAAACCAGAACGTGACGGCCTTTTCTGCGCCCGTATCTTTGGGCCGGTAAAAGA
TTACGAGTGCCTGTGCGGTAAGTACAAGCGCCTGAAACACCGTGGCGTCATCTGTGAGAAGTGCGGCGTTGAAGTGACCCAGACTAAAGTACGCCGTGAG
CGTATGGGCCACATCGAACTGGCTTCCCCGACTGCGCACATCTGGTTCCTGAAATCGCTGCCGTCCCGTATCGGTCTGCTGCTCGATATGCCGCTGCGCG
ATATCGAACGCGTACTGTACTTTGAATCCTATGTGGTTATCGAAGGCGGTATGACCAACCTGGAACGTCAGCAGATCCTGACTGAAGAGCAGTATCTGGA
CGCGCTGGAAGAGTTCGGTGACGAATTCGACGCGAAGATGGGGGCGGAAGCAATCCAGGCTCTGCTGAAGAGCATGGATCTGGAGCAAGAGTGCGAACAG
CTGCGTGAAGAGCTGAACGAAACCAACTCCGAAACCAAGCGTAAAAAGCTGACCAAGCGTATCAAACTGCTGGAAGCGTTCGTTCAGTCTGGTAACAAAC
CAGAGTGGATGATCCTGACCGTTCTGCCGGTACTGCCGCCAGATCTGCGTCCGCTGGTTCCGCTGGATGGTGGTCGTTTCGCGACTTCTGACCTGAACGA
TCTGTATCGTCGCGTCATTAACCGTAACAACCGTCTGAAACGTCTGCTGGATCTGGCTGCGCCGGACATCATCGTACGTAACGAAAAACGTATGCTGCAG
GAAGCGGTAGACGCCCTGCTGGATAACGGTCGTCGCGGTCGTGCGATCACCGGTTCTAACAAGCGTCCTCTGAAATCTTTGGCCGACATGATCAAAGGTA
AACAGGGTCGTTTCCGTCAGAACCTGCTCGGTAAGCGTGTTGACTACTCCGGTCGTTCTGTAATCACCGTAGGTCCATACCTGCGTCTGCATCAGTGCGG
TCTGCCGAAGAAAATGGCACTGGAGCTGTTCAAACCGTTCATCTACGGCAAGCTGGAACTGCGTGGTCTTGCTACCACCATTAAAGCTGCGAAGAAAATG
GTTGAGCGCGAAGAAGCTGTCGTTTGGGATATCCTGGACGAAGTTATCCGCGAACACCCGGTACTGCTGAACCGTGCACCGACTCTGCACCGTCTGGGTA
TCCAGGCATTTGAACCGGTACTGATCGAAGGTAAAGCTATCCAGCTGCACCCGCTGGTTTGTGCGGCATATAACGCCGACTTCGATGGTGACCAGATGGC
TGTTCACGTACCGCTGACGCTGGAAGCCCAGCTGGAAGCGCGTGCGCTGATGATGTCTACCAACAACATCCTGTCCCCGGCGAACGGCGAACCAATCATC
GTTCCGTCTCAGGACGTTGTACTGGGTCTGTACTACATGACCCGTGACTGTGTTAACGCCAAAGGCGAAGGCATGGTGCTGACTGGCCCGAAAGAAGCAG
AACGTCTGTATCGCTCTGGTCTGGCTTCTCTGCATGCGCGCGTTAAAGTGCGTATCACCGAGTATGAAAAAGATGCTAACGGTGAATTAGTAGCGAAAAC
CAGCCTGAAAGACACGACTGTTGGCCGTGCCATTCTGTGGATGATTGTACCGAAAGGTCTGCCTTACTCCATCGTCAACCAGGCGCTGGGTAAAAAAGCA
ATCTCCAAAATGCTGAACACCTGCTACCGCATTCTCGGTCTGAAACCGACCGTTATTTTTGCGGACCAGATCATGTACACCGGCTTCGCCTATGCAGCGC
GTTCTGGTGCATCTGTTGGTATCGATGACATGGTCATCCCGGAGAAGAAACACGAAATCATCTCCGAGGCAGAAGCAGAAGTTGCTGAAATTCAGGAGCA
GTTCCAGTCTGGTCTGGTAACTGCGGGCGAACGCTACAACAAAGTTATCGATATCTGGGCTGCGGCGAACGATCGTGTATCCAAAGCGATGATGGATAAC
CTGCAAACTGAAACCGTGATTAACCGTGACGGTCAGGAAGAGAAGCAGGTTTCCTTCAACAGCATCTACATGATGGCCGACTCCGGTGCGCGTGGTTCTG
CGGCACAGATTCGTCAGCTTGCTGGTATGCGTGGTCTGATGGCGAAGCCGGATGGCTCCATCATCGAAACGCCAATCACCGCGAACTTCCGTGAAGGTCT
GAACGTACTCCAGTACTTCATCTCCACCCACGGTGCTCGTAAAGGTCTGGCGGATACCGCACTGAAAACTGCGAACTCCGGTTACCTGACTCGTCGTCTG
GTTGACGTGGCGCAGGACCTGGTGGTTACCGAAGACGATTGTGGTACCCATGAAGGTATCATGATGACTCCGGTTATCGAGGGTGGTGACGTTAAAGAGC
CGCTGCGCGATCGCGTACTGGGTCGTGTAACTGCTGAAGACGTTCTGAAGCCGGGTACTGCTGATATCCTCGTTCCGCGCAACACGCTGCTGCACGAACA
GTGGTGTGACCTGCTGGAAGAGAACTCTGTCGACGCGGTTAAAGTACGTTCTGTTGTATCTTGTGACACCGACTTTGGTGTATGTGCGCACTGCTACGGT
CGTGACCTGGCGCGTGGCCACATCATCAACAAGGGTGAAGCAATCGGTGTTATCGCGGCACAGTCCATCGGTGAACCGGGTACACAGCTGACCATGCGTA
CGTTCCACATCGGTGGTGCGGCATCTCGTGCGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGT
GAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGT
GCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAACCGTTGCAAACTGGGACCCGCACACCATGCCGGTTATCACCGAAGTAAGCGGTT
TTGTACGCTTTACTGACATGATCGACGGCCAGACCATTACGCGTCAGACCGACGAACTGACCGGTCTGTCTTCGCTGGTGGTTCTGGATTCCGCAGAACG
TACCGCAGGTGGTAAAGATCTGCGTCCGGCACTGAAAATCGTTGATGCTCAGGGTAACGACGTTCTGATCCCAGGTACCGATATGCCAGCGCAGTACTTC
CTGCCGGGTAAAGCGATTGTTCAGCTGGAAGATGGCGTACAGATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACA
TCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAA
AGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCGGTAGACGGTAGCGATCCGTACGAAGAGATGATTCCGAAATGGCGTCAGCTCAACGTGTTCGAA
GGTGAACGTGTAGAACGTGGTGACGTAATTTCCGACGGTCCGGAAGCGCCGCACGACATTCTGCGTCTGCGTGGTGTTCATGCTGTTACTCGTTACATCG
TTAACGAAGTACAGGACGTATACCGTCTGCAGGGCGTTAAGATTAACGATAAACACATCGAAGTTATCGTTCGTCAGATGCTGCGTAAAGCTACCATCGT
TAACGCGGGTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCA
ACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGCGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCG
AAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACCA
GGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGAACGCAGGT
CTGGGCGGTTCTGATAACGAGTAA

Loop counts:

3 nts: 9
4 nts: 15
5 nts: 14
6 nts: 11
7 nts: 7
8 nts: 3
9 nts: 1
10 nts: 2

Tetra-loop variants:

CCAU    1
AUAU    1
GUAU    1
AAGC    1
GAAA    1
GGAU    1
UCCA    1
CGUG    1
AUCG    1
AAUC    1
GUUA    1
UCCG    1
GAAG    1
GUGA    1
CUGU    1

Single bulge variants:

G x 0 bulge: 5
A x 0 bulge: 8
U x 0 bulge: 17
C x 0 bulge: 14

1 x 1 internal loop variants:

G x G bulge: 4
G x A bulge: 5
G x U bulge: 0
G x C bulge: 0
A x G bulge: 5
A x A bulge: 3
A x U bulge: 0
A x C bulge: 8
U x G bulge: 0
U x A bulge: 0
U x U bulge: 4
U x C bulge: 4
C x G bulge: 0
C x A bulge: 8
C x U bulge: 4
C x C bulge: 1