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 
GAATTCTTTGTGACTGGCAGGCATTCAGACCAATAGTGATTAGGAAACCTTGAAGCCTGCCCAACGATCGTGGGCAGGAGGTGGTTTCTGGTTTGTTGGG
GCGTGTGTATGTGTATTTGGGGGGACTGAAGGGTACGTGGGGCGAAACAAAACCGGCCATGGCAGCAGCGGAGGAGGAGGACGGGGGCCCCGAAGGGCCA
AATCGCGAGCGGGGCGGGGCGGGCGCGACCTTCGAATGTAATATATGTTTGGAGACTGCTCGGGAAGCTGTGGTCAGTGTGTGTGGCCACCTGTACTGTT
GGCCATGTCTTCATCAGTGGCTGGAGACACGGCCAGAACGGCAAGAGTGTCCAGTATGTAAAGCTGGGATCAGCAGAGAGAAGGTTGTCCCGCTTTATGG
GCGAGGGAGCCAGAAGCCCCAGGATCCCAGATTAAAAACTCCACCCCGCCCCCAGGGCCAGAGACCAGCTCCGGAGAGCAGAGGGGGATTCCAGCCATTT
GGTGATACCGGGGGCTTCCACTTCTCATTTGGTGTTGGTGCTTTTCCCTTTGGCTTTTTCACCACCGTCTTCAATGCCCATGAGCCTTTCCGCCGGGGTA
CAGGTGTGGATCTGGGACAGGGTCACCCAGCCTCCAGCTGGCAGGATTCCCTCTTCCTGTTTCTCGCCATCTTCTTCTTTTTTTGGCTGCTCAGTATTTG
AGCTATGTCTGCTTCCTGCCCACCTCCAGCCAGAGAAGAATCAGTATTGAGGGTCCCTGCTGACCCTTCCGTACTCCTGGACCCCCTTGACCCCTCTATT
TCTGTTGGCTAAGGCCAGCCCTGGACATTGTCCAGGAAGGCCTGGGGAGGAGGAGTGAAGTCTGTGCATAGATGGGAGAGCCTTCTGCTCAGAGGCTCAC
TCAGTAACGTTGTTTAATTCTCTGCCCTGGGGAAGGAGGATGGATTGAGAGAATGTCTTTCTCCTCTCCTAAGTCTTTGCTTTCCCTGATTTCTTGATTT
GATCTTCAAAGGTGGGCAAAGTTCCCTCTGACTCTTCCCCCACTCCCCATCTTACTGATTTAATTTAATTTTTCACTCCCCAGAGTCTAATATGGATTCT
GACTCTTAAGTGCTTCCGCCCCCTCACTACCTCCTTTAATACAAATTCAATAAAAAAGGTGAAATATA

Loop counts:

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

Tetra-loop variants:

UAAG    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