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

ATGCCTGTTATAACTCTTCCTGATGGCAGCCAACGCCATTACGATCACGCTGTAAGCCCCATGGATGTTGCGCTGGACATTGGTCCAGGTCTGGCGAAAG
CCTGTATCGCAGGGCGCGTTAATGGCGAACTGGTTGATGCTTGCGATCTGATTGAAAACGACGCACAACTGTCGATCATTACCGCCAAAGACGAAGAAGG
TCTGGAGATCATTCGTCACTCCTGTGCGCACCTGTTAGGGCACGCGATTAAACAACTTTGGCCGCATACCAAAATGGCAATCGGCCCGGTTATTGACAAC
GGTTTTTATTACGACGTTGATCTTGACCGCACGTTAACCCAGGAAGATGTCGAAGCACTCGAGAAGCGGATGCATGAGCTTGCTGAGAAAAACTACGACG
TCATTAAGAAGAAAGTCAGCTGGCACGAAGCGCGTGAAACTTTCGCCAACCGTGGGGAGAGCTACAAAGTCTCCATTCTTGACGAAAACATCGCCCATGA
TGACAAGCCAGGTCTGTACTTCCATGAAGAATATGTCGATATGTGCCGCGGTCCGCACGTACCGAACATGCGTTTCTGCCATCATTTCAAACTAATGAAA
ACGGCAGGGGCTTACTGGCGTGGCGACAGCAACAACAAAATGTTGCAACGTATTTACGGTACGGCGTGGGCAGACAAAAAAGCACTTAACGCTTACCTGC
AGCGCCTGGAAGAAGCCGCGAAACGCGACCACCGTAAAATCGGTAAACAGCTCGACCTGTACCATATGCAGGAAGAAGCGCCGGGTATGGTATTCTGGCA
CAACGACGGCTGGACCATCTTCCGTGAACTGGAAGTGTTTGTTCGTTCTAAACTGAAAGAGTACCAGTATCAGGAAGTTAAAGGTCCGTTCATGATGGAC
CGTGTCCTGTGGGAAAAAACCGGTCACTGGGACAACTACAAAGATGCAATGTTCACCACATCTTCTGAGAACCGTGAATACTGCATTAAGCCGATGAACT
GCCCGGGTCACGTACAAATTTTCAACCAGGGGCTGAAGTCTTATCGCGATCTGCCGCTGCGTATGGCCGAGTTTGGTAGCTGCCACCGTAACGAGCCGTC
AGGTTCGCTGCATGGCCTGATGCGCGTGCGTGGATTTACCCAGGATGACGCGCATATCTTCTGTACTGAAGAACAAATTCGCGATGAAGTTAACGGATGT
ATCCGTTTAGTCTATGATATGTACAGCACTTTTGGCTTCGAGAAGATCGTCGTCAAACTCTCCACTCGTCCTGAAAAACGTATTGGCAGCGACGAAATGT
GGGATCGTGCTGAGGCGGACCTGGCGGTTGCGCTGGAAGAAAACAACATCCCGTTTGAATATCAACTGGGTGAAGGCGCTTTCTACGGTCCGAAAATTGA
ATTTACCCTGTATGACTGCCTCGATCGTGCATGGCAGTGCGGTACAGTACAGCTGGACTTCTCTTTGCCGTCTCGTCTGAGCGCTTCTTATGTAGGCGAA
GACAATGAACGTAAAGTACCGGTAATGATTCACCGCGCAATTCTGGGGTCGATGGAACGTTTCATCGGTATCCTGACCGAAGAGTTCGCTGGTTTCTTCC
CGACCTGGCTTGCGCCGGTTCAGGTTGTTATCATGAATATTACCGATTCACAGTCTGAATACGTTAACGAATTGACGCAAAAACTATCAAATGCGGGCAT
TCGTGTTAAAGCAGACTTGAGAAATGAGAAGATTGGCTTTAAAATCCGCGAGCACACTTTGCGTCGCGTCCCATATATGCTGGTCTGTGGTGATAAAGAG
GTGGAATCAGGCAAAGTTGCCGTTCGCACCCGCCGTGGTAAAGACCTGGGAAGCATGGACGTAAATGAAGTGATCGAGAAGCTGCAACAAGAGATTCGCA
GCCGCAGTCTTAAACAATTGGAGGAATAA

Loop counts:

4 nts: 5
5 nts: 4
6 nts: 4
7 nts: 2

Tetra-loop variants:

GUCA    1
UGUA    1
AAGU    1
UGGA    1
AUUG    1

Single bulge variants:

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

1 x 1 internal loop variants:

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