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 
AAAGGAGCCAAGACCATGGCGAAAGCCGGGGATAAGAGCAGCAGCAGCGGGAAGAAAAGTCTAAAACGGAAAGCCGCTGCCGAAGAACTTCAGGAGGCTG
CAGGCGCTGGGGATGGGGCGACGGAAAACGGGGTCCAACCCCCGAAAGCGGCTGCCTTTCCGCCAGGCTTTAGCATTTCGGAGATTAAAAACAAACAGCG
GCGACACTTAATGTTCACGCGGTGGAAACAGCAGCAGCGGAAGGAAAAGTTGGCAGCTAAGAAAAAACTTAAAAAAGAAAGAGAGGCTCTTGGCGATAAG
GCTCCACCAAAGCCTGTACCCAAGACCATTGACAACCAGCGAGTGTATGATGAAACCACAGTAGACCCTAATGATGAAGAGGTCGCTTATGATGAAGCTA
CAGATGAATTTGCTTCTTACTTCAACAAACAGACTTCTCCCAAGATTCTCATCACAACATCAGATAGACCTCATGGGAGAACAGTACGACTCTGTGAACA
GCTCTCCACAGTTATACCAAACTCACATGTTTATTACAGAAGAGGACTGGCTCTGAAAAAAATTATTCCACAGTGCATCGCAAGAGATTTCACAGACCTG
ATTGTTATTAATGAAGATCGTAAAACCCCAAATGGACTTATTTTGAGTCACTTGCCAAATGGCCCAACTGCTCATTTTAAAATGAGCAGTGTTCGTCTTC
GTAAAGAAATTAAGAGAAGAGGCAAGGACCCCACAGAACACATACCTGAAATAATTCTGAATAATTTTACAACACGGCTGGGTCATTCAATTGGACGTAT
GTTTGCATCTCTCTTTCCTCATAATCCTCAATTTATCGGAAGGCAGGTTGCCACATTCCACAATCAACGGGATTACATATTCTTCAGATTTCACAGATAC
ATATTCAGGAGTGAAAAGAAAGTGGGAATTCAGGAACTTGGACCACGTTTTACCTTAAAATTAAGGTCTCTTCAGAAAGGAACCTTTGATTCTAAATATG
GAGAGTATGAATGGGTCCATAAGCCCCGGGAAATGGATACAAGTAGAAGAAAATTCCATTTATAAAGTACTGAGAGAATGATATTGGATTTTGCTGAACA
GGCCTATCTTGAACTTTGGTAAATTATTTTTGACAGAATACTCTTTTCAAAATGGCATTTGCTGATTTCATAAACCTTTCACGTCTGGACGAATTACCAA
ATGCCATGAATTGCCACTGTGTGTTTATGTAGAAAATACAAATAAAAGTTATTTTGATGGCTTAGGTTTCCTTAAACTTAGTTCTCTTGTTTTTGGGTAA
CTGTGAATAATTAAGTTGGAATCAAGATTCAGATTAACTTTCCTATTTGCATAGAACACATGAGAGGAATAAAATGGTTGGTAAA

Loop counts:

4 nts: 2
6 nts: 1
7 nts: 1
8 nts: 1

Tetra-loop variants:

UUAA    1
AAAU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 2
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