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

ATGGAAAAGACATATAACCCACAAGATATCGAACAGCCGCTTTACGAGCACTGGGAAAAGCAGGGCTACTTTAAGCCTAATGGCGATGAAAGCCAGGAAA
GTTTCTGCATCATGATCCCGCCGCCGAACGTCACCGGCAGTTTGCATATGGGTCACGCCTTCCAGCAAACCATCATGGATACCATGATCCGCTATCAGCG
CATGCAGGGCAAAAACACCCTGTGGCAGGTCGGTACTGACCACGCCGGGATCGCTACCCAGATGGTCGTTGAGCGCAAGATTGCCGCAGAAGAAGGTAAA
ACCCGTCACGACTACGGCCGCGAAGCTTTCATCGACAAAATCTGGGAATGGAAAGCGGAATCTGGCGGCACCATTACCCGTCAGATGCGCCGTCTCGGCA
ACTCCGTCGACTGGGAGCGTGAACGCTTCACCATGGACGAAGGCCTGTCCAATGCGGTGAAAGAAGTTTTCGTTCGTCTGTATAAAGAAGACCTGATTTA
CCGTGGCAAACGCCTGGTAAACTGGGATCCGAAACTGCGCACCGCTATCTCTGACCTGGAAGTCGAAAACCGCGAATCGAAAGGTTCGATGTGGCACATC
CGCTATCCGCTGGCTGACGGTGCGAAAACCGCAGACGGTAAAGATTATCTGGTGGTCGCGACTACCCGTCCAGAAACCCTGCTGGGCGATACTGGCGTAG
CCGTTAACCCGGAAGATCCGCGTTACAAAGATCTGATTGGCAAATATGTCATTCTGCCGCTGGTTAACCGTCGTATTCCGATCGTTGGCGACGAACACGC
CGACATGGAAAAAGGCACCGGCTGCGTGAAAATCACTCCGGCGCACGACTTTAACGACTATGAAGTGGGTAAACGTCACGCCCTGCCGATGATCAACATC
CTGACCTTTGACGGCGATATCCGTGAAAGCGCCCAGGTGTTCGATACCAAAGGTAACGAATCTGACGTTTATTCCAGCGAAATCCCTGCAGAGTTCCAGA
AACTGGAGCGTTTTGCTGCACGTAAAGCAGTCGTTGCCGCAGTTGACGCGCTTGGCCTGCTGGAAGAAATTAAACCGCACGACCTGACCGTTCCTTACGG
CGACCGTGGCGGCGTAGTTATCGAACCAATGCTGACCGACCAGTGGTACGTGCGTGCCGATGTCCTGGCGAAACCGGCGGTTGAAGCGGTTGAGAACGGC
GACATTCAGTTCGTACCGAAGCAGTACGAAAACATGTACTTCTCCTGGATGCGCGATATTCAGGACTGGTGTATCTCTCGTCAGTTGTGGTGGGGTCACC
GTATCCCGGCATGGTATGACGAAGCGGGTAACGTTTATGTTGGCCGCAACGAAGACGAAGTGCGTAAAGAAAATAACCTCGGTGCTGATGTTGTCCTGCG
TCAGGACGAAGACGTTCTCGATACCTGGTTCTCTTCTGCGCTGTGGACCTTCTCTACCCTTGGCTGGCCGGAAAATACCGACGCCCTGCGTCAGTTCCAC
CCAACCAGCGTGATGGTATCTGGTTTCGACATCATTTTCTTCTGGATTGCCCGCATGATCATGATGACCATGCACTTCATCAAAGATGAAAATGGCAAAC
CGCAGGTGCCGTTCCACACCGTTTACATGACCGGCCTGATTCGTGATGACGAAGGCCAGAAGATGTCCAAATCCAAGGGTAACGTTATCGACCCACTGGA
TATGGTTGACGGTATTTCGCTGCCAGAACTGCTGGAAAAACGTACCGGCAATATGATGCAGCCGCAGCTGGCGGACAAAATCCGTAAGCGCACCGAGAAG
CAGTTCCCGAACGGTATTGAGCCGCACGGTACTGACGCGCTGCGCTTCACCCTGGCGGCGCTGGCGTCTACCGGTCGTGACATCAACTGGGATATGAAGC
GTCTGGAAGGTTACCGTAACTTCTGTAACAAGCTGTGGAACGCCAGCCGCTTTGTGCTGATGAACACAGAAGGTCAGGATTGCGGCTTCAACGGCGGCGA
AATGACGCTGTCGCTGGCGGACCGCTGGATTCTGGCGGAGTTCAACCAGACCATCAAAGCGTACCGCGAAGCGCTGGACAGCTTCCGCTTCGATATCGCC
GCAGGCATTCTGTATGAGTTCACCTGGAACCAGTTCTGTGACTGGTATCTCGAGCTGACCAAGCCGGTAATGAACGGTGGCACCGAAGCAGAACTGCGCG
GTACTCGCCATACGCTGGTGACTGTACTGGAAGGTCTGCTGCGCCTCGCGCATCCGATCATTCCGTTCATCACCGAAACCATCTGGCAGCGTGTGAAAGT
ACTTTGCGGTATCACTGCCGACACCATCATGCTGCAGCCGTTCCCGCAGTACGATGCATCTCAGGTTGATGAAGCCGCACTGGCCGACACCGAATGGCTG
AAACAGGCGATCGTTGCGGTACGTAACATCCGTGCAGAAATGAACATCGCGCCGGGCAAACCGCTGGAGCTGCTGCTGCGTGGTTGCAGCGCGGATGCAG
AACGTCGCGTAAATGAAAACCGTGGCTTCCTGCAAACCCTGGCGCGTCTGGAAAGTATCACCGTGCTGCCTGCCGATGACAAAGGTCCGGTTTCCGTTAC
GAAGATCATCGACGGTGCAGAGCTGCTGATCCCGATGGCTGGCCTCATCAACAAAGAAGATGAGCTGGCGCGTCTGGCGAAAGAAGTGGCGAAGATTGAA
GGTGAAATCAGCCGTATCGAGAACAAACTGGCGAACGAAGGCTTTGTCGCCCGCGCACCGGAAGCGGTCATCGCGAAAGAGCGTGAGAAGCTGGAAGGCT
ATGCGGAAGCGAAAGCGAAACTGATTGAACAGCAGGCTGTTATCGCCGCGCTGTAA

Loop counts:

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

Tetra-loop variants:

AUCG    1
CUGU    1
AAAC    1
GAAA    1
AAUA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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