Annotated gene sequence

Experiment = in vitro 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

GCAAATTGCCCTAGTAACGGCCGCATGGTAACTCAGGCGCCGGGCGCACTGTCCTAGCTGCTGGTTTTCCACGCTGGTTTTAGCTCCCGGCGTCTGCAAA
ATGAAGATTGAGGAGGTGAAGAGCACTACGAAGACGCAGCGCATCGCCTCCCACAGCCACGTGAAAGGGCTGGGGCTGGACGAGAGCGGCTTGGCCAAGC
AGGCGGCCTCAGGGCTTGTGGGCCAGGAGAACGCGCGAGAGGCATGTGGCGTCATAGTAGAATTAATCAAAAGCAAGAAAATGGCTGGAAGAGCTGTCTT
GTTGGCAGGACCTCCTGGAACTGGCAAGACAGCTCTGGCTCTGGCTATTGCTCAGGAGCTGGGTAGTAAGGTCCCCTTCTGCCCAATGGTGGGGAGTGAA
GTTTACTCAACTGAGATCAAGAAGACAGAGGTGCTGATGGAGAACTTCCGCAGGGCCATTGGGCTGCGAATAAAGGAGACCAAGGAAGTTTATGAAGGTG
AAGTCACAGAGCTAACTCCGTGTGAGACAGAGAATCCCATGGGAGGATATGGCAAAACCATTAGCCATGTGATCATAGGACTCAAAACAGCCAAAGGAAC
CAAACAGTTGAAACTGGACCCCAGCATTTTTGAAAGTTTGCAGAAAGAGCGAGTAGAAGCTGGAGATGTGATTTACATTGAAGCCAACAGTGGGGCCGTG
AAGAGGCAGGGCAGGTGTGATACCTATGCCACAGAATTCGACCTTGAAGCTGAAGAGTATGTCCCCTTGCCAAAAGGGGATGTGCACAAAAAGAAAGAAA
TCATCCAAGATGTGACCTTGCATGACTTGGATGTGGCTAATGCGCGGCCCCAGGGGGGACAAGATATCCTGTCCATGATGGGCCAGCTAATGAAGCCAAA
GAAGACAGAAATCACAGACAAACTTCGAGGGGAGATTAATAAGGTGGTGAACAAGTACATCGACCAGGGCATTGCTGAGCTGGTCCCGGGTGTGCTGTTT
GTTGATGAGGTCCACATGCTGGACATTGAGTGCTTCACCTACCTGCACCGCGCCCTGGAGTCTTCTATCGCTCCCATCGTCATCTTTGCATCCAACCGAG
GCAACTGTGTCATCAGAGGCACTGAGGACATCACATCCCCTCACGGCATCCCTCTTGACCTTCTGGACCGAGTGATGATAATCCGGACCATGCTGTATAC
TCCACAGGAAATGAAACAGATCATTAAAATCCGTGCCCAGACGGAAGGAATCAACATCAGTGAGGAGGCACTGAACCACCTGGGGGAGATTGGCACCAAG
ACCACACTGAGGTACTCAGTGCAGCTGCTGACCCCGGCCAACTTGCTTGCTAAAATCAACGGGAAGGACAGCATTGAGAAAGAGCATGTCGAAGAGATCA
GTGAACTTTTCTATGATGCCAAGTCCTCCGCCAAAATCCTGGCTGACCAGCAGGATAAGTACATGAAGTGAGATGGCTGAGGTTTTCAGCAGTAAGAGAC
TCCCCAGGTGTGCCTGGCCTGGGTCCAGCCTGTGGGCGCTTGCCCCTGGGCTTGGGGCTGCCGTCCCCACTCAGGCGTGGTCTGCAGCGCTGTCAGTTCA
GTGTGGAAAGCATTTCTTTTTAAGTTATCGTAACTGTTCCTGTGGTTGCTTTGAAAGAACCCTTCCTTACCTGGTGTGTTTTCTATAAATCTTCATAGGT
TATTTTGATTCTCTCTCTCTCTCTCTCTAAGTTTTTTAAAAATAAACTTTTCAGAACAGTT

Loop counts:

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

Tetra-loop variants:

ACCU    2
AAGA    1
UCAU    1
UUUU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 1
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: 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: 0