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

GCAGCCTGGGGATTAGGACCCGGAGTTGCCAAGGTGTCAGCACTCTTTGCTCTTGAATTGATTAAAAAGTCTAATCAAATGCATATATTTTCTTCAAACA
AGTTTTACCCGAAAGTTTGTTGAAAGAGGCTAAATCAGGGAGTTCTTTGCGTCTGCAAGGCGGCTTTTTAGTTCTGGATTCTTTTCCGGCTTATTCTAAG
ACACCTATGAGTCGTGGGGCTTCTCTCGCGAAGTCTTTAAGTGGACAGTACGCATGCGCCAACTTCCTCTTTTTCCGGCTGGAACCATGGAGGGTGTAGA
AGAGAAGAAGAAGGAGGTTCCTGCTGTGCCAGAAACCCTTAAGAAAAAGCGAAGGAATTTCGCAGAGCTGAAGATCAAGCGCCTGAGAAAGAAGTTTGCC
CAAAAGATGCTTCGAAAGGCAAGGAGGAAGCTTATCTATGAAAAAGCAAAGCACTATCACAAGGAATATAGGCAGATGTACAGAACTGAAATTCGAATGG
CGAGGATGGCAAGAAAAGCTGGCAACTTCTATGTACCTGCAGAACCCAAATTGGCGTTTGTCATCAGAATCAGAGGTATCAATGGAGTGAGCCCAAAGGT
TCGAAAGGTGTTGCAGCTTCTTCGCCTTCGTCAAATCTTCAATGGAACCTTTGTGAAGCTCAACAAGGCTTCGATTAACATGCTGAGGATTGTAGAGCCA
TATATTGCATGGGGGTACCCCAATCTGAAGTCAGTAAATGAACTAATCTACAAGCGTGGTTATGGCAAAATCAATAAGAAGCGAATTGCTTTGACAGATA
ACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGCATGGAGGATTTGATTCATGAGATCTATACTGTTGGAAAACGCTTCAAAGAGGCAAA
TAACTTCCTGTGGCCCTTCAAATTGTCTTCTCCACGAGGTGGAATGAAGAAAAAGACCACCCATTTTGTAGAAGGTGGAGATGCTGGCAACAGGGAGGAC
CAGATCAACAGGCTTATTAGAAGAATGAACTAAGGTGTCTACCATGATTATTTTTCTAAGCTGGTTGGTTAATAAACAGTACCTGCTCTCAAATTGAAAT
A

Loop counts:

3 nts: 2
4 nts: 4
6 nts: 1

Tetra-loop variants:

CGAA    1
GGCU    1
CAAA    1
GUCU    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: 1
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