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 
GTGACCGGCCAACACTGAGTGTTGTCTCGCTCTGGCGTCAGAGCCGTCGTGGCTCGTTCCATTCTCGGCGGTGGTACCTGCTCCCGGTGGCCCTGAGGAC
GTGTGGGCCAGGGGCGGCCCCGAAATTAGGAAGCGGAGGGGGAGCAGTCTGCAGGTCTGCGGGGCTAAGTGTCGCGGCGGCGCACCTCGCGTCAAGAATC
CGGAGGAGGAGACTGCAAGGATAGGCCCAGGAGTAATGGAGTCCAAAGAGGAACTAGCGGCAAACAATCTCAACGGGGAAAATGCCCAACAAGAAAACGA
AGGAGGGGAGCAGGCCCCCACGCAGAATGAAGAAGAATCCCGCCATTTGGGAGGGGGTGAAGGCCAGAAGCCTGGAGGAAATATCAGGCGGGGGCGAGTT
AGGCGACTTGTCCCTAATTTTCGATGGGCCATACCTAATAGGCATATTGAGCACAATGAAGCGAGAGATGATGTAGAAAGGTTTGTAGGGCAGATGATGG
AAATCAAGAGAAAGACTAGGGAACAGCAGATGAGGCACTATATGCGCTTCCAAACTCCTGAACCTGACAACCATTATGACTTTTGCCTCATACCTTGAAT
CCTAAAAGTTTTCGCTGAGGTTAATGTGAACACTGCTTTACAAGCTTGTATTTTTGTGATTTACTTTTTCTGTAAGCCTTTTGGGGTTTACACTTACCAG
TTTCTAATGGAAATTAGAATTCTAATTGAATATTGTTTTGTCTCAGCCTAAAAGTTACGGTCAGCATGGCAATTCACCTATTTTAGGAAAAATACTCTTT
TCATAATATGAAATGCATAAAGCAGTTCAAAAAGCAGTCTGTATTCCATCATCTTCCTTTTTCATTCCAGTCCTTATTTTTGTAAGTATTACTTTTCCTC
CTCCGGCTACCTGGACTCAAAATCTCAGTTGTCTTTGACAGTTTTTTTCTTGTCCCTGACCAAAAAAGAATGATCATACCCAGAATTCAATGTTTGATAT
TTTAAGAATGTATGTTCTAGTGTTTTTCAGAGTGAGTCTACCATCTGTATAAAAACACCTTGGGGGCAGGCAGGGGCATTTAAAAATGTAGGACCTATCG
TCCAGACTCACAGAGTGGGGCTCCAGAATCTCCATTTTTAACAAACTCTCTTAAGTAATTCTGATGTGTACCAAAATCAGTGCCATTGGTGTGTGTGTAC
GTAACTATATACATATGTGTGTGTGTGTATATATATAATGTGTCATAACCGTAAACAATAAACAATATCAAGATAAATCTGACTTTGATGGGCAAGTAAT
TAAAAAAGAAAAGTATGAGACCTTAAAA

Loop counts:

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

Tetra-loop variants:

AGGC    1
UUUG    1
GGAA    1
UUUU    1
GUAU    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: 1
G x U bulge: 0
G x C bulge: 0
A x G bulge: 1
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: 1