Annotated gene sequence

Experiment = in vivo icSHAPE / NAI-N3 RefSeq = hg38 Cell = HEK293T Original Data Reference = Cell. 2016;165(5):1267-1279.

stable secondary structure loop bulge/internal loop no SHAPE data coding sequence

AAATCCTTCCTTCCCCGGGGTAGAAGTCCAGGGTGAGAAATTGGTTCCGAACTCAAAGGAACCCAGTGCCGGGCCACAGCCGGGTCACGTGGCCGGCGGC
CCCCCATGACGTGCTGGCTGCGGGGCGTCACGGCGACGTTCGGGCGACCTGCCGAGTGGCCAGGCTACCTCAGTCACCTGTGTGGTCGCAGTGCTGCCAT
GGACCTGGGACCCATGCGCAAGAGTTACCGCGGGGACCGAGAGGCATTTGAGGAGACTCATCTGACCTCCCTTGACCCAGTGAAACAGTTTGCTGCCTGG
TTTGAGGAGGCTGTTCAGTGTCCTGACATAGGGGAAGCCAATGCCATGTGTCTGGCTACCTGCACCAGAGATGGAAAACCCTCTGCTCGCATGTTGCTGC
TGAAGGGCTTCGGGAAAGATGGCTTCCGCTTCTTCACTAACTTCGAGAGTCGAAAAGGAAAAGAGCTGGACTCTAATCCCTTTGCTTCCCTTGTCTTCTA
CTGGGAGCCACTTAACCGTCAGGTGCGTGTGGAAGGCCCTGTGAAGAAACTGCCTGAGGAGGAGGCTGAGTGCTACTTCCACTCCCGCCCCAAGAGCAGC
CAGATTGGGGCTGTGGTCAGCCACCAGAGTTCTGTGATCCCTGATCGGGAGTATCTGAGAAAGAAAAATGAGGAACTGGAACAGCTCTACCAGGATCAAG
AGGTGCCCAAGCCAAAATCCTGGGGTGGCTATGTCCTGTACCCTCAGGTGATGGAGTTCTGGCAAGGTCAAACCAACCGCCTGCATGACCGGATAGTCTT
TCGGCGGGGCCTACCCACAGGAGATTCCCCTTTGGGGCCCATGACCCACCGCGGGGAGGAAGACTGGCTCTATGAGAGACTTGCACCTTAACTCTGGGAC
CTGCTGGCCCAGAGTGGAGCTAGGGCTAGGTGTCAAGAGAGGGTGTGGGATTGGGACCCAGGCCCTTCTTTCTAAACTCAACCCATTTCCCTCCCTACCC
CTTATCTTCAGGACTCTTCAGAGCTAATCCTCTAAGTTCTCTGTACTCAGTTGGTTCTCAGTTAGCTGGTCAAGTGGAGTGTAATGGTGGCGTAGAGAAT
CACAAATGGAAAATAATTCCATAATTATTTTTTTGACCTTGCCTATGATTGATTAGGATAGCTCCCTCTAGGGGTAGCAGCCGGTGTGACTCCCTTTCTG
GTGACAGACAGGGCCCCAGCAGCCCTGTCTGTTACCATGTGAGTCATACTGGCCAAAGCTTAGTCCTAGCATATGCACCTGAGCCAACCTGGCCAATCAG
ATTGTTTTGTCAATAATTTGAAATTTGAACTGGAGAGATCCAGAACCTTGGGAGTCATTAAAGCCAAGTCATTCATAGCAGCCAGGAAACAATAGGAACC
AAAAGCCTCTGCCTGCTGCTATTGCAATTCCCAGGATCTCTCCTTCCCTGGATCCCTCCCTCCCAGGTCTGGGCTGTGCAGTTCCTCCCCCTGCCTTAAA
ACACCCCACTATCTCTGTAAAGTCTCTCTCTCTCTTTTTTTTTTTTTTACTTAATCTAGCTAGAATCTATTTCTGTTGATTACAACTTAACTAACTCATT
TACGGATAGGACTTTTTTTTTTCTTTTTTTCTTTTTTCTTTTCTTTTTTTTTTTTGAGATGGAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGTGT
GATCTTGGCTCACTGCAACCTCTGCCTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCACACGCCACCACACCCAA
CTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGATTGTCTCCATCTCTTGACCTTGTGATCCACCCACCTCAGCCTCCCAAAGT
GCTGGGATTACAGGCATGAGCCACCACACCCAGCGAGACGGGGTTTCATTATGTTGGCCAGGCTGGTCTCCAACTCCTGACCTAAAGTGATCTGCCCGCC
TTGGCCTCCCAAAGTGCTGGGATTACAGACATGAGCCACCACGCTTGGCCGGGATAGTATATTTTTATAGCACTTCCCCTACTGATTGCTGCCTTCTCTG
TGGCTACAAGGGACCCACAGAATTACAGGGAAGTTACAGGGAAGCAGGTTTCATCTCAATATTGGGAGAGATTTCAAACAATCACACCTGCCTGAGAAGG
AGTGGGCTGTCACTAGGAATTTTTATTCCCAGTCCGTCAGGAATTTTGTAGAAGGGCTTCATGTGCTGGTACCAATAGGACAGGAAGATTTTAATCAGCT
TTACTATCTATGTTTTTTTATGGAAACTGTGTGTATGTATACATACATTTTCCAAAAAGAAAAATTAAATGATTATAGAGATTATGTTTTTCAGACT

Loop counts:

4 nts: 2

Tetra-loop variants:

UUAU    1
UGUA    1

Single bulge variants:

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