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

ATGCAGGTCAGCAGAAGGCAGTTCTTTAAGATCTGCGCTGGCGGTATGGCAGGCACCACGGCAGCGGCACTGGGTTTTGCACCCAGCGTAGCACTCGCGG
AAACCCGGCAGTATAAACTGCTGCGCACCCGCGAAACCCGTAATACCTGCACCTATTGTTCCGTAGGCTGTGGGCTGTTGATGTACAGCCTCGGTGACGG
AGCAAAAAACGCCAAAGCATCTATCTTCCATATCGAAGGCGATCCGGATCACCCGGTCAACCGCGGTGCACTTTGTCCGAAAGGCGCTGGCCTGGTGGAT
TTCATCCACTCCGAAAGCCGTCTGAAGTTTCCGGAATACCGTGCGCCAGGTTCTGATAAATGGCAGCAAATCAGTTGGGAAGAGGCGTTTGATCGCATCG
CCAAACTGATGAAAGAAGACCGCGATGCTAACTACATTGCGCAAAACGCCGAAGGCGTGACTGTTAACCGCTGGCTCTCCACCGGGATGCTGTGTGCTTC
CGCGTCGAGTAACGAAACCGGCTATTTAACGCAAAAATTCTCCCGCGCGCTGGGTATGCTCGCGGTCGACAACCAGGCGCGTGTCTGACACGGACCAACG
GTAGCAAGTCTTGCTCCAACATTTGGTCGCGGTGCGATGACCAACCACTGGGTCGACATCAAGAACGCCAACCTCGTCGTGGTGATGGGCGGTAACGCCG
CTGAAGCTCACCCGGTCGGGTTCCGCTGGGCGATGGAAGCCAAAATTCACAACGGCGCGAAGCTGATTGTGATCGATCCTCGCTTTACGCGTACGGCGGC
GGTAGCTGACTACTATGCCCCTATTCGTTCCGGTACTGACATTGCTTTCCTGTCAGGCGTATTGCTGTACCTGCTGAACAATGAAAAATTCAACCGCGAA
TACACCGAAGCCTATACCAACGCCAGCCTGATCGTGCGTGAGGATTACGGCTTTGAAGATGGCCTGTTCACCGGCTACGACGCGGAAAAACGCAAGTACG
ATAAATCCTCCTGGACTTATGAACTGGACGAAAACGGCTTCGCCAAACGCGATACCACGCTGCAACATCCGCGCTGCGTGTGGAACTTGCTGAAACAGCA
CGTTTCCCGCTACACGCCAGATGTGGTTGAAAACATCTGTGGTACGCCAAAAGACGCGTTCCTGAAAGTCTGCGAATACATCGCAGAAACCAGTGCTCAC
GATAAAACTGCCTCGTTCCTGTATGCCCTCGGCTGGACGCAACACTCCGTTGGTGCGCAAAACATTCGTACGATGGCGATGATCCAGCTGCTGCTCGGCA
ATATGGGGATGGCAGGCGGCGGCGTTAACGCCCTGCGCGGTCACTCCAATATTCAGGGGCTGACGGACCTGGGGCTGCTGTCGCAGAGCCTGCCAGGTTA
CATGACGCTGCCAAGCGAGAAGCAGACCGATCTGCAAACCTACCTTACCGCCAACACGCCAAAACCGCTGCTGGAAGGCCAGGTAAACTACTGGGGCAAC
TACCCGAAATTCTTCGTCTCTATGATGAAGGCCTTCTTTGGTGATAAAGCGACGGCGGAAAATAGCTGGGGCTTTGACTGGTTGCCGAAGTGGGATAAAG
GCTACGACGTCCTGCAATACTTCGAGATGATGAAAGAGGGCAAGGTCAATGGCTATATCTGCCAGGGCTTTAACCCTGTTGCCTCATTCCCGAACAAAAA
CAAAGTGATCGGTTGTCTGTCGAAACTGAAGTTCCTCGTCACCATCGACCCACTGAACACTGAAACCTCTAACTTCTGGCAGAACCACGGTGAGCTGAAC
GAAGTTGACTCGTCGAAGATCCAGACCGAAGTGTTCCGTCTGCCATCGACCTGCTTCGCGGAAGAGAACGGTTCTATCGTTAACTCAGGTCGCTGGTTAC
AGTGGCACTGGAAAGGTGCGGACGCCCCGGGGATTGCGCTGACTGACGGCGAGATCCTCTCCGGTATCTTCCTGCGCTTGCGCAAGATGTATGCCGAACA
GGGTGGCGCGAACCCGGACCAGGTGCTGAACATGACATGGAACTACGCCATTCCGCATGAGCCATCTTCAGAAGAAGTGGCGATGGAGAGCAACGGTAAG
GCGCTGGCCGATATTACCGATCCGGCAACCGGTGCGGTTATCGTCAAGAAAGGCCAACAACTTAGTTCGTTCGCCCAATTGCGCGATGACGGTACAACCT
CCTGTGGCTGCTGGATTTTCGCCGGTAGCTGGACGCCGGAAGGCAACCAGATGGCACGCCGTGATAACGCCGATCCGTCTGGCCTCGGTAACACGCTGGG
CTGGGCATGGGCATGGCCGCTTAACCGCCGCATTCTGTATAACCGCGCCTCCGCAGATCCGCAGGGTAACCCGTGGGATCCGAAGCGTCAGTTGCTGAAA
TGGGACGGCACTAAGTGGACCGGCTGGGATATTCCGGACTACAGCGCAGCGCCTCCGGGTAGCGGCGTCGGGCCGTTTATCATGCAGCAGGAAGGCATGG
GGCGTCTGTTTGCCCTCGATAAGATGGCGGAAGGTCCGTTCCCGGAACACTACGAGCCGTTTGAAACGCCGCTGGGAACTAACCCGCTGCATCCAAACGT
TATCTCGAACCCGGCTGCACGTATCTTTAAAGACGACGCCGAAGCATTGGGTAAAGCCGATAAGTTCCCGTATGTCGGAACCACCTATCGTCTGACCGAG
CACTTCCACTACTGGACCAAACACGCGCTGTTGAACGCGATTTTGCAGCCAGAGCAGTTTGTGGAAATCGGGGAGTCGCTGGCGAATAAACTTGGCATTG
CCCAGGGCGATACCGTGAAAGTCTCCTCCAACCGTGGCTATATCAAAGCCAAAGCGGTGGTGACCAAACGTATTCGCACGCTGAAAGCGAACGGCAAAGA
TATCGATACCATCGGTATTCCGATTCACTGGGGCTATGAAGGCGTAGCTAAAAAAGGCTTTATTGCCAATACTTTAACGCCATTCGTTGGTGATGCGAAC
ACGCAGACGCCGGAGTTTAAGTCCTTCCTTGTGAATGTGGAAAAGGTGTAA

Loop counts:

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

Tetra-loop variants:

AUAA    1
CCGA    1
CUUG    1
AGAA    1
AUAU    1
AACA    1
CUGA    1

Single bulge variants:

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

1 x 1 internal loop variants:

G x G bulge: 2
G x A bulge: 2
G x U bulge: 0
G x C bulge: 0
A x G bulge: 2
A x A bulge: 0
A x U bulge: 0
A x C bulge: 3
U x G bulge: 0
U x A bulge: 0
U x U bulge: 1
U x C bulge: 1
C x G bulge: 0
C x A bulge: 3
C x U bulge: 1
C x C bulge: 1