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

GGAAAACGGCCAGCCTGAGGAGCTGCTGCGAGGGTCCGCTTCGTCTTTCGAGAGTGACTCCCGCGGTCCCAAGGCTTTCCAGAGCGAACCTGTGCGGCTG
CAGGCACCGGCGTGTTGAGTTTCCGGCGTTCCGAAGGACTGAGCTCTTGTCGCGGATCCCGTCCGCCGTTTCCAGCCCCCAGTCTCAGAGCGGAGCCCAC
AGAGCAGGGCACCGGCATGGCCAAAGCCGCGGCGATCGGCATCGACCTGGGCACCACCTACTCCTGCGTGGGGGTGTTCCAACACGGCAAGGTGGAGATC
ATCGCCAACGACCAGGGCAACCGCACCACCCCCAGCTACGTGGCCTTCACGGACACCGAGCGGCTCATCGGGGATGCGGCCAAGAACCAGGTGGCGCTGA
ACCCGCAGAACACCGTGTTTGACGCGAAGCGGCTGATTGGCCGCAAGTTCGGCGACCCGGTGGTGCAGTCGGACATGAAGCACTGGCCTTTCCAGGTGAT
CAACGACGGAGACAAGCCCAAGGTGCAGGTGAGCTACAAGGGGGAGACCAAGGCATTCTACCCCGAGGAGATCTCGTCCATGGTGCTGACCAAGATGAAG
GAGATCGCCGAGGCGTACCTGGGCTACCCGGTGACCAACGCGGTGATCACCGTGCCGGCCTACTTCAACGACTCGCAGCGCCAGGCCACCAAGGATGCGG
GTGTGATCGCGGGGCTCAACGTGCTGCGGATCATCAACGAGCCCACGGCCGCCGCCATCGCCTACGGCCTGGACAGAACGGGCAAGGGGGAGCGCAACGT
GCTCATCTTTGACCTGGGCGGGGGCACCTTCGACGTGTCCATCCTGACGATCGACGACGGCATCTTCGAGGTGAAGGCCACGGCCGGGGACACCCACCTG
GGTGGGGAGGACTTTGACAACAGGCTGGTGAACCACTTCGTGGAGGAGTTCAAGAGAAAACACAAGAAGGACATCAGCCAGAACAAGCGAGCCGTGAGGC
GGCTGCGCACCGCCTGCGAGAGGGCCAAGAGGACCCTGTCGTCCAGCACCCAGGCCAGCCTGGAGATCGACTCCCTGTTTGAGGGCATCGACTTCTACAC
GTCCATCACCAGGGCGAGGTTCGAGGAGCTGTGCTCCGACCTGTTCCGAAGCACCCTGGAGCCCGTGGAGAAGGCTCTGCGCGACGCCAAGCTGGACAAG
GCCCAGATTCACGACCTGGTCCTGGTCGGGGGCTCCACCCGCATCCCCAAGGTGCAGAAGCTGCTGCAGGACTTCTTCAACGGGCGCGACCTGAACAAGA
GCATCAACCCCGACGAGGCTGTGGCCTACGGGGCGGCGGTGCAGGCGGCCATCCTGATGGGGGACAAGTCCGAGAACGTGCAGGACCTGCTGCTGCTGGA
CGTGGCTCCCCTGTCGCTGGGGCTGGAGACGGCCGGAGGCGTGATGACTGCCCTGATCAAGCGCAACTCCACCATCCCCACCAAGCAGACGCAGATCTTC
ACCACCTACTCCGACAACCAACCCGGGGTGCTGATCCAGGTGTACGAGGGCGAGAGGGCCATGACGAAAGACAACAATCTGTTGGGGCGCTTCGAGCTGA
GCGGCATCCCTCCGGCCCCCAGGGGCGTGCCCCAGATCGAGGTGACCTTCGACATCGATGCCAACGGCATCCTGAACGTCACGGCCACGGACAAGAGCAC
CGGCAAGGCCAACAAGATCACCATCACCAACGACAAGGGCCGCCTGAGCAAGGAGGAGATCGAGCGCATGGTGCAGGAGGCGGAGAAGTACAAAGCGGAG
GACGAGGTGCAGCGCGAGAGGGTGTCAGCCAAGAACGCCCTGGAGTCCTACGCCTTCAACATGAAGAGCGCCGTGGAGGATGAGGGGCTCAAGGGCAAGA
TCAGCGAGGCGGACAAGAAGAAGGTTCTGGACAAGTGTCAAGAGGTCATCTCGTGGCTGGACGCCAACACCTTGGCCGAGAAGGACGAGTTTGAGCACAA
GAGGAAGGAGCTGGAGCAGGTGTGTAACCCCATCATCAGCGGACTGTACCAGGGTGCCGGTGGTCCCGGGCCTGGCGGCTTCGGGGCTCAGGGTCCCAAG
GGAGGGTCTGGGTCAGGCCCTACCATTGAGGAGGTGGATTAGGGGCCTTTGTTCTTTAGTATGTTTGTCTTTGAGGTGGACTGTTGGGACTCAAGGACTT
TGCTGCTGTTTTCCTATGTCATTTCTGCTTCAGCTCTTTGCTGCTTCACTTCTTTGTAAAGTTGTAACCTGATGGTAATTAGCTGGCTTCATTATTTTTG
TAGTACAACCGATATGTTCATTAGAATTCTTTGCATTTAATGTTGATACTGTAAGGGTGTTTCGTTCCCTTTAAATGAATCAACACTGCCACCTTCTGTA
CGAGTTTGTTTGTTTTTTTTTTTTTTTTTTTTTTTTGCTTGGCGAAAACACTACAAAGGCTGGGAATGTATGTTTTTATAATTTGTTTATTTAAATATGA
AAAATAAAATGTTAAACTTTT

Loop counts:

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

Tetra-loop variants:

AAGA    1
UGUG    1
AAGU    1
UGGC    1
CAAA    1
GAUU    1
GCUG    1
GGAC    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 5
U x 0 bulge: 2
C x 0 bulge: 1

1 x 1 internal loop variants:

G x G bulge: 1
G x A bulge: 4
G x U bulge: 0
G x C bulge: 0
A x G bulge: 4
A x A bulge: 0
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: 0
C x G bulge: 0
C x A bulge: 2
C x U bulge: 0
C x C bulge: 1