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 
CGTCACCGCCGCGCAGCGCGGGCGCAGAGCCCTGCCCTCAGCTGAAGGGAGTCTTCTTTTTTTTTTTTTTTTCCGCTGTTTTTTTCTCCGCCCCTAAGAG
GTTGACTCCAAACCCGGAGTTCCGCTAGGTCCAACAGGAGGGCTTACGGCGTGAGCGGCGTACCTGGGGAGAGGCTTAGGCAGCGGCAACCGCTGATTGG
CAGTAAAGGGGTTCACTCCCCATCTCCTGCTCGGGCGAAACCGGGACAGCCAATCAGAGAGAGTACTGACGGAAACGGCCCAATCCTGGAGCAGGGCTGA
GGGAGGGGGCGGGGACAAATGGCTCAGGTGGACTCCGGGCTGGAGCTGTCCTGGGGGAGCTTGTTTGCGGCAGCGGCTGCTGCTGCCACTGCTGTGCTGG
GGGCCCGGTCGCCAGGCAAAAAGCCCTCCCACGTTTGAGGGGAGTCATGAGCCGTTTCCTGAATGTGTTAAGAAGTTGGCTGGTTATGGTGTCCATCATA
GCCATGGGGAACACGCTGCAGAGCTTCCGAGACCACACTTTTCTCTATGAAAAGCTCTACACTGGCAAGCCAAACCTTGTGAATGGCCTCCAAGCTCGGA
CCTTTGGGATCTGGACGCTGCTCTCATCAGTGATTCGCTGCCTCTGTGCCATTGACATTCACAACAAGACGCTCTATCACATCACACTCTGGACCTTCCT
CCTTGCCCTGGGGCATTTCCTCTCTGAGTTGTTTGTCTATGGAACTGCAGCTCCCACGATTGGCGTCCTGGCACCCCTGATGGTGGCAAGTTTCTCCATC
CTGGGTATGCTGGTCGGGCTCCGGTATCTAGAAGTAGAACCAGTATCCAGACAGAAGAAGAGAAACTGAGGCCAGCATTATCACCTCCAGGACTTTCTCG
TTTTCCACCTTGGCCATCTTCTTCCTTCGTCGTCTCTCCTCTTTAATTTCTTTTCTATTCCATCATCTGCCCTTTTATTCACTTTTAGCCTCTTTTTTTA
ATTTTTAAAATTTAAAGATATGCATACTGAAAAGTATATAACATGTACGTACAATTTAAAGAATAATTTTAAAGTGAATACTACGTAACTCCATCCAAGT
CAAGAAATTGCCAGCTTCTCGGAAGCCCACTGTGTCTCCTTCCCCTACCTGCAACCTCTTCCAGGCTCCCTTTTCCAGCCTTCCCCTTTTTCCCTTTTAT
TTTCATGCCTTGATTTGACTTGTGTGGTGGGAACATGTGAACTATGAAACTTAAACCTGCTGCCCACCCAGAGCAGCTGTGACCAAGGGCTGCCTCAAGG
GGTTGTCCACGCAGGTTGGGCTCCTCTCTGCTGCTGGACCCAAGACTCTGAACCTTCCAAGGGACAGGCAGTTCTTCTAAGAAGGGCTCCCCTGTGTGTG
AGCAAGACCACAGCTCTCCTTCTATCTACAGATGCATGAGGGTTGGAAGAGTCTGGGCTGTTTTTAGACCTTCTGGTCAGCTGTATTTGTGTAACAACTT
TTGTAATAAATAGAAAAACCCTCTGCTCTGATCAGTTCTTGTACTTTGACCTCTGCTAAGACAAGAGCATGGCTGCCTCCTCTGAGCCCTAGGAGAATCA
CAGCTTTATGCCTGATTGAATACACCATAGTGAGTAGGACAGCTCATGACACAGGTCAGCCTGGCTGCCTCCGGCTCCTTACTGTCATTTGCTCATTCCT
CTTGTATTCTTGAAGTCAAATCTTCTTTTTTCTCACCTTCAAGAGTCTGCGTTCACAACTAAACACTAAGTGCCCTTTCTTATTTCCTCCTAAAGAAGAA
ACAGATTCTTGAGAGAGCAGAGACAAAAAAATAGAACTAGGCAGCATAGATGAAACAACTGCATGACATGGGAAGAAGACAACTAAACCCCGAGGAGAAT
GCACTGGAATGGACAGTTGCTCTTAAACCCTACCCAGAGGGCCTCCCCCAGCTGGACCCTCATACACAGTGTGTGTATCCAAAAGGCCATTGCTATTTCA
GCAAATATTTGTTGAGTACTTCTCCATGCCGGACACTTGGGAAAGAGAAATGAACGACACAGGCAATGCCCCTGCCCTGTGGGCCTTATATTATAGTCAA
GGTAACAGAATCAACAAGCCAACACAAAAATAAAGAACTTCAAATAGGGATAAGAACTCTAACAAACACAAGGTATTTTGGTCAAGAAGGAATGTGGGGT
GGGCAGTGGGGAACGTAACTTAAATTAGATCATCAGAAAGTCCTCCCTGAGGAGATGGGATTTTTTTGTTTTTTAGAGACAGGGTTTCACTCTGTCACCC
AGGCTGGAGTGCAGTGGCACAATCACACCTCACTGCAGCCTCAACTTCCTGGGCTCAAGTGATCCTCCTGCATCAGCTTCCCAAGTAGCTGGGACTACAA
GTGTGTACCACCACATCCAGCTAACATTTTTGGGGGTGGGAAGAGATGGGGTCTTACTATGTTGTCCAGGCTAAGAGGTGGGATTTGAGCTGAGACTTGA
ATGCCCAGGAGTTAAATGTCTTAAGATATGGAGCAGGCCGTTAGAAAGGAGGGAGCAGCAACTGGAAGGTAGAATAGTCTTATTCAAGGAATAAGAACTA
TGTAATCACAGCATGGTGAAGAGTTAGGAAGTG

Loop counts:

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

Tetra-loop variants:

GUCC    1
GAAG    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