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 
ATTTTGCGAACGGCGAGCAGCGGCGGCGGCGCGGAGAGACGCAGCGGAGGTTTTCCTGGTTTCGGACCCCAGCGGCCGGATGGTGAAATCCTCCCTGCAG
CGGATCCTCAATAGCCACTGCTTCGCCAGAGAGAAGGAAGGGGATAAACCCAGCGCCACCATCCACGCCAGCCGCACCATGCCGCTCCTAAGCCTGCACA
GCCGCGGCGGCAGCAGCAGTGAGAGTTCCAGGGTCTCCCTCCACTGCTGTAGTAACCCGGGTCCGGGGCCTCGGTGGTGCTCCGATGCCCCTCACCCACC
CCTGAAGATCCCAGGTGGGCGAGGGAATAGTCAGAGGGATCACAATCTTTCAGCTAACTTATTCTACTCCGATGATCGGCTGAATGTAACAGAGGAACTA
ACGTCCAACGACAAGACGAGGATTCTCAACGTCCAGTCCAGGCTCACAGACGCCAAACGCATTAACTGGCGAACAGTGCTGAGTGGCGGCAGCCTCTACA
TCGAGATCCCGGGCGGCGCGCTGCCCGAGGGGAGCAAGGACAGCTTTGCAGTTCTCCTGGAGTTCGCTGAGGAGCAGCTGCGAGCCGACCATGTCTTCAT
TTGCTTCCACAAGAACCGCGAGGACAGAGCCGCCTTGCTCCGAACCTTCAGCTTTTTGGGCTTTGAGATTGTGAGACCGGGGCATCCCCTTGTCCCCAAG
AGACCCGACGCTTGCTTCATGGCCTACACGTTCGAGAGAGAGTCTTCGGGAGAGGAGGAGGAGTAGGGCCGCCTCGGGGCTGGGCATCCGGCCCCTGGGG
CCACCCCTTGTCAGCCGGGTGGGTAGGAACCGTAGACTCGCTCATCTCGCCTGGGTTTGTCCGCATGTTGTAATCGTGCAAATAAACGCTCACTCCGAAT
TAGCGGTGTATTTCTTGAAGTTTAATATTGTGTTTGTGATACTGAAGTATTTGCTTTAATTCTAAATAAAAATTTATATTTTACTTTTTTATTGCTGGTT
TAAGATGATTCAGATTATCCTTGTACTTTGAGGAGAAGTTTCTTATTTGGAGTCTTTTGGAAACAGTCTTAGTCTTTTAACTTGGAAAGATGAGGTATTA
ATCCCCTCCATTGCTCTCCAAAAGCCAATAAAGTGATTACACCCGATG

Loop counts:

4 nts: 6
5 nts: 1
6 nts: 1
7 nts: 1
9 nts: 2

Tetra-loop variants:

UCAG    1
CCUA    1
GGUC    1
CACA    1
CGCG    1
GCAU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 1
U x 0 bulge: 1
C x 0 bulge: 1

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: 1
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