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

ATGCGTCTGGATCGTCTTACTAATAAATTCCAGCTTGCTCTTGCCGATGCCCAATCACTTGCACTCGGGCACGACAACCAATTTATCGAACCACTTCATT
TAATGAGCGCCCTGCTGAATCAGGAAGGGGGTTCGGTTAGTCCTTTATTAACATCCGCTGGCATAAATGCTGGCCAGTTGCGCACAGATATCAATCAGGC
ATTAAATCGTTTACCGCAGGTTGAAGGTACTGGTGGTGATGTCCAGCCATCACAGGATCTGGTGCGCGTTCTTAATCTTTGCGACAAGCTGGCGCAAAAA
CGTGGTGATAACTTTATCTCGTCAGAACTGTTCGTTCTGGCGGCACTTGAGTCTCGCGGCACGCTGGCCGACATCCTGAAAGCAGCAGGGGCGACCACCG
CCAACATTACTCAAGCGATTGAACAAATGCGTGGAGGTGAAAGCGTGAACGATCAAGGTGCTGAAGACCAACGTCAGGCTTTGAAAAAATATACCATCGA
CCTTACCGAACGAGCCGAACAGGGCAAACTCGATCCGGTGATTGGTCGTGATGAAGAAATTCGCCGTACCATTCAGGTGCTGCAACGTCGTACTAAAAAT
AACCCGGTACTGATTGGTGAACCCGGCGTCGGTAAAACTGCCATCGTTGAAGGTCTGGCGCAGCGTATTATCAACGGCGAAGTGCCGGAAGGGTTGAAAG
GCCGCCGGGTACTGGCGCTGGATATGGGCGCGCTGGTGGCTGGGGCGAAATATCGCGGTGAGTTTGAAGAACGTTTAAAAGGCGTGCTTAACGATCTTGC
CAAACAGGAAGGCAACGTCATCCTATTTATCGACGAATTACATACCATGGTCGGCGCGGGTAAAGCCGATGGCGCAATGGACGCCGGAAACATGCTGAAA
CCGGCGCTGGCGCGTGGTGAATTGCACTGCGTAGGTGCCACGACGCTTGACGAATATCGCCAGTACATTGAAAAAGATGCTGCGCTGGAACGTCGTTTCC
AGAAAGTGTTTGTTGCCGAGCCTTCTGTTGAAGATACCATTGCGATTCTGCGTGGCCTGAAAGAACGTTACGAATTGCACCACCATGTGCAAATTACTGA
CCCGGCAATTGTTGCAGCGGCGACGTTGTCTCATCGCTACATTGCTGACCGTCAGCTGCCGGATAAAGCCATCGACCTGATCGATGAAGCAGCATCCAGC
ATTCGTATGCAGATTGACTCAAAACCAGAAGAACTCGACCGACTCGATCGTCGTATCATCCAGCTCAAACTGGAACAACAGGCGTTAATGAAAGAGTCTG
ATGAAGCCAGTAAAAAACGTCTGGATATGCTCAACGAAGAACTGAGCGACAAAGAACGTCAGTACTCCGAGTTAGAAGAAGAGTGGAAAGCAGAGAAGGC
ATCGCTTTCTGGTACGCAGACCATTAAAGCGGAACTGGAACAGGCGAAAATCGCTATTGAACAGGCTCGCCGTGTGGGGGACCTGGCGCGGATGTCTGAA
CTGCAATACGGCAAAATCCCGGAACTGGAAAAGCAACTGGAAGCCGCAACGCAGCTCGAAGGCAAAACTATGCGTCTGTTGCGTAATAAAGTGACCGACG
CCGAAATTGCTGAAGTGCTGGCGCGTTGGACGGGGATTCCGGTTTCTCGCATGATGGAAAGCGAGCGCGAAAAACTGCTGCGTATGGAGCAAGAACTGCA
CCATCGCGTAATTGGTCAGAACGAAGCGGTTGATGCGGTATCTAACGCTATTCGTCGTAGCCGTGCGGGGCTGGCGGATCCAAATCGCCCGATTGGTTCA
TTCCTGTTCCTCGGCCCAACTGGTGTGGGGAAAACAGAGCTTTGTAAGGCGCTGGCGAACTTTATGTTTGATAGCGACGAGGCGATGGTCCGTATCGATA
TGTCCGAGTTTATGGAGAAACACTCGGTGTCTCGTTTGGTTGGTGCGCCTCCGGGATATGTCGGTTATGAAGAAGGTGGCTACCTGACCGAAGCGGTGCG
TCGTCGTCCGTATTCCGTCATCCTGCTGGATGAAGTGGAAAAAGCGCATCCGGATGTCTTCAACATTCTGTTGCAGGTACTGGATGATGGGCGTCTGACT
GACGGGCAAGGGAGAACGGTCGACTTCCGTAATACGGTCGTCATTATGACCTCTAACCTCGGTTCCGATCTGATTCAGGAACGCTTCGGTGAACTGGATT
ATGCGCACATGAAAGAGCTGGTGCTCGGTGTGGTAAGCCATAACTTCCGTCCGGAATTCATTAACCGTATCGATGAAGTGGTGGTCTTCCATCCGCTGGG
TGAACAGCACATTGCCTCGATTGCGCAGATTCAGTTGAAACGTCTGTACAAACGTCTGGAAGAACGTGGTTATGAAATCCACATTTCTGACGAGGCGCTG
AAACTGCTGAGCGAGAACGGTTACGATCCGGTCTATGGTGCACGTCCTCTGAAACGTGCAATTCAGCAGCAGATCGAAAACCCGCTGGCACAGCAAATAC
TGTCTGGTGAATTGGTTCCGGGTAAAGTGATTCGCCTGGAAGTTAATGAAGACCGGATTGTCGCCGTCCAGTAA

Loop counts:

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

Tetra-loop variants:

GGCU    1
UGCU    1
GUGA    1
GCGA    1
UAAA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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