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

ATGTCTGAGAAAACTTTTCTGGTGGAAATCGGCACTGAAGAGCTGCCACCAAAAGCACTGCGCAGCCTGGCTGAGTCCTTTGCTGCGAACTTTACTGCGG
AGCTGGATAACGCTGGCCTCGCACACGGCACCGTTCAATGGTTTGCTGCTCCGCGTCGTCTGGCGCTGAAAGTAGCTAACCTGGCGGAAGCGCAACCGGA
TCGTGAAATCGAAAAACGCGGCCCGGCGATTGCCCAGGCGTTCGACGCTGAAGGCAAACCGAGCAAAGCGGCAGAAGGTTGGGCGCGTGGTTGCGGTATT
ACCGTTGACCAGGCTGAGCGTCTGACTACCGATAAAGGCGAATGGCTGCTGTATCGCGCCCATGTGAAGGGCGAAAGCACCGAAGCACTGCTGCCGAATA
TGGTTGCGACTTCTCTGGCGAAACTGCCGATCCCGAAACTGATGCGTTGGGGCGCAAGCGACGTGCACTTCGTGCGTCCGGTGCACACCGTGACCCTGCT
GCTGGGCGACAAAGTCATTCCGGCAACCATTCTGGGCATTCAGTCCGATCGCGTGATTCGCGGCCACCGCTTTATGGGCGAGCCGGAATTCACCATCGAT
AACGCCGATCAGTATCCGGAAATTCTGCGTGAGCGTGGGAAAGTCATCGCCGATTACGAAGAACGTAAGGCGAAGATTAAAGCCGATGCCGAAGAAGCAG
CGCGTAAGATTGGCGGTAACGCTGACTTAAGCGAAAGCCTGCTGGAAGAAGTGGCTTCGCTGGTGGAGTGGCCGGTCGTTCTGACCGCAAAATTCGAAGA
GAAATTCCTCGCGGTGCCGGCTGAAGCGCTGGTTTACACCATGAAAGGTGACCAGAAATACTTCCCGGTGTATGCGAACGACGGCAAACTGCTGCCGAAC
TTTATCTTCGTTGCCAACATCGAATCGAAAGATCCGCAGCAGATTATCTCCGGTAACGAGAAAGTCGTTCGTCCGCGTCTGGCGGATGCCGAGTTCTTCT
TCAACACCGACCGTAAAAAACGTCTTGAAGATAACCTGCCGCGCCTGCAAACCGTGTTGTTCCAGCAACAGTTGGGGACGCTGCGCGACAAAACTGACCG
CATCCAGGCGCTGGCTGGCTGGATTGCTGAACAGATTGGCGCTGACGTTAACCACGCTACCCGTGCGGGTCTGCTGTCTAAGTGCGACCTGATGACCAAC
ATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGT
ATCAGCCGCGTTTTGCTGGTGATGACCTGCCGTCCAACCCAGTAGCTTGTGCGCTGGCGATTGCTGACAAGATGGATACCCTGGCGGGTATCTTCGGTAT
CGGTCAGCATCCGAAAGGCGACAAAGACCCGTTTGCGCTGCGTCGTGCCGCGCTTGGCGTGCTGCGAATTATCGTTGAGAAGAACCTCAACCTTGATCTG
CAAACGCTGACCGAAGAAGCGGTGCGTCTGTATGGCGATAAGCTGACTAATGCCAACGTAGTTGATGATGTTATCGACTTTATGCTCGGTCGCTTCCGCG
CCTGGTATCAGGACGAAGGTTATACCGTTGACACCATCCAGGCGGTACTGGCGCGTCGTCCGACTCGTCCGGCTGATTTCGATGCCCGTATGAAAGCGGT
ATCGCATTTCCGTACCCTGGATGCAGCTGCTGCACTGGCGGCGGCGAACAAACGTGTATCTAACATTCTGGCGAAATCTGACGAAGTGCTGAGCGACCGC
GTGAATGCCTCTACCCTGAAAGAGCCGGAAGAAATTAAACTGGCGATGCAGGTTGTGGTGCTACGTGACAAGCTGGAGCCGTACTTTACGGAAGGTCGTT
ACCAGGATGCGCTGGTCGAACTGGCTGAGCTGCGTGAACCGGTTGATGCTTTCTTCGATAAAGTGATGGTCATGGTTGATGACAAAGAATTGCGTATCAA
CCGTCTGACCATGCTGGAGAAACTGCGCGAACTGTTCCTGCGCGTTGCGGATATTTCGCTGTTGCAATAA

Loop counts:

3 nts: 4
4 nts: 4
5 nts: 2
6 nts: 3

Tetra-loop variants:

UGGC    1
GUCU    1
ACUG    1
CCAA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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