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

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

Tetra-loop variants:

AUCG    1
CUGU    1
GUAC    1
GCGU    1
AAAC    1
GAAA    1

Single bulge variants:

G x 0 bulge: 2
A x 0 bulge: 2
U x 0 bulge: 3
C x 0 bulge: 7

1 x 1 bulge 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: 4
U x G bulge: 0
U x A bulge: 0
U x U bulge: 1
U x C bulge: 0
C x G bulge: 0
C x A bulge: 4
C x U bulge: 0
C x C bulge: 1