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

ATGTCAGAACGTTTCCCAAATGACGTGGATCCGATCGAAACTCGCGACTGGCTCCAGGCGATCGAATCGGTCATCCGTGAAGAAGGTGTTGAGCGTGCTC
AGTATCTGATCGACCAACTGCTTGCTGAAGCCCGCAAAGGCGGTGTAAACGTAGCCGCAGGCACAGGTATCAGCAACTACATCAACACCATCCCCGTTGA
AGAACAACCGGAGTATCCGGGTAATCTGGAACTGGAACGCCGTATTCGTTCAGCTATCCGCTGGAACGCCATCATGACGGTGCTGCGTGCGTCGAAAAAA
GACCTCGAACTGGGCGGCCATATGGCGTCCTTCCAGTCTTCCGCAACCATTTATGATGTGTGCTTTAACCACTTCTTCCGTGCACGCAACGAGCAGGATG
GCGGCGACCTGGTTTACTTCCAGGGCCACATCTCCCCGGGCGTGTACGCTCGTGCTTTCCTGGAAGGTCGTCTGACTCAGGAGCAGCTGGATAACTTCCG
TCAGGAAGTTCACGGCAATGGCCTCTCTTCCTATCCGCACCCGAAACTGATGCCGGAATTCTGGCAGTTCCCGACCGTATCTATGGGTCTGGGTCCGATT
GGTGCTATTTACCAGGCTAAATTCCTGAAATATCTGGAACACCGTGGCCTGAAAGATACCTCTAAACAAACCGTTTACGCGTTCCTCGGTGACGGTGAAA
TGGACGAACCGGAATCCAAAGGTGCGATCACCATCGCTACCCGTGAAAAACTGGATAACCTGGTCTTCGTTATCAACTGTAACCTGCAGCGTCTTGACGG
CCCGGTCACCGGTAACGGCAAGATCATCAACGAACTGGAAGGCATCTTCGAAGGTGCTGGCTGGAACGTGATCAAAGTGATGTGGGGTAGCCGTTGGGAT
GAACTGCTGCGTAAGGATACCAGCGGTAAACTGATCCAGCTGATGAACGAAACCGTTGACGGCGACTACCAGACCTTCAAATCGAAAGATGGTGCGTACG
TTCGTGAACACTTCTTCGGTAAATATCCTGAAACCGCAGCACTGGTTGCAGACTGGACTGACGAGCAGATCTGGGCACTGAACCGTGGTGGTCACGATCC
GAAGAAAATCTACGCTGCATTCAAGAAAGCGCAGGAAACCAAAGGCAAAGCGACAGTAATCCTTGCTCATACCATTAAAGGTTACGGCATGGGCGACGCG
GCTGAAGGTAAAAACATCGCGCACCAGGTTAAGAAAATGAACATGGACGGTGTGCGTCATATCCGCGACCGTTTCAATGTGCCGGTGTCTGATGCAGATA
TCGAAAAACTGCCGTACATCACCTTCCCGGAAGGTTCTGAAGAGCATACCTATCTGCACGCTCAGCGTCAGAAACTGCACGGTTATCTGCCAAGCCGTCA
GCCGAACTTCACCGAGAAGCTTGAGCTGCCGAGCCTGCAAGACTTCGGCGCGCTGTTGGAAGAGCAGAGCAAAGAGATCTCTACCACTATCGCTTTCGTT
CGTGCTCTGAACGTGATGCTGAAGAACAAGTCGATCAAAGATCGTCTGGTACCGATCATCGCCGACGAAGCGCGTACTTTCGGTATGGAAGGTCTGTTCC
GTCAGATTGGTATTTACAGCCCGAACGGTCAGCAGTACACCCCGCAGGACCGCGAGCAGGTTGCTTACTATAAAGAAGACGAGAAAGGTCAGATTCTGCA
GGAAGGGATCAACGAGCTGGGCGCAGGTTGTTCCTGGCTGGCAGCGGCGACCTCTTACAGCACCAACAATCTGCCGATGATCCCGTTCTACATCTATTAC
TCGATGTTCGGCTTCCAGCGTATTGGCGATCTGTGCTGGGCGGCTGGCGACCAGCAAGCGCGTGGCTTCCTGATCGGCGGTACTTCCGGTCGTACCACCC
TGAACGGCGAAGGTCTGCAGCACGAAGATGGTCACAGCCACATTCAGTCGCTGACTATCCCGAACTGTATCTCTTACGACCCGGCTTACGCTTACGAAGT
TGCTGTCATCATGCATGACGGTCTGGAGCGTATGTACGGTGAAAAACAAGAGAACGTTTACTACTACATCACTACGCTGAACGAAAACTACCACATGCCG
GCAATGCCGGAAGGTGCTGAGGAAGGTATCCGTAAAGGTATCTACAAACTCGAAACTATTGAAGGTAGCAAAGGTAAAGTTCAGCTGCTCGGCTCCGGTT
CTATCCTGCGTCACGTCCGTGAAGCAGCTGAGATCCTGGCGAAAGATTACGGCGTAGGTTCTGACGTTTATAGCGTGACCTCCTTCACCGAGCTGGCGCG
TGATGGTCAGGATTGTGAACGCTGGAACATGCTGCACCCGCTGGAAACTCCGCGCGTTCCGTATATCGCTCAGGTGATGAACGACGCTCCGGCAGTGGCA
TCTACCGACTATATGAAACTGTTCGCTGAGCAGGTCCGTACTTACGTACCGGCTGACGACTACCGCGTACTGGGTACTGATGGCTTCGGTCGTTCCGACA
GCCGTGAGAACCTGCGTCACCACTTCGAAGTTGATGCTTCTTATGTCGTGGTTGCGGCGCTGGGCGAACTGGCTAAACGTGGCGAAATCGATAAGAAAGT
GGTTGCTGACGCAATCGCCAAATTCAACATCGATGCAGATAAAGTTAACCCGCGTCTGGCGTAA

Loop counts:

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

Tetra-loop variants:

GUCC    1
UGAU    1
AACG    1
UGAC    1
GUCA    1
GCUC    1
AAUU    1

Single bulge variants:

G x 0 bulge: 2
A x 0 bulge: 2
U x 0 bulge: 2
C x 0 bulge: 6

1 x 1 internal loop variants:

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