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

GTGGAGTCCCCGCAGGCAGAGACGCGGAGTGGGGGTGGCGGGTCGCCGGATCGGGTGGGAAGTAAAAGACCCCCAGGAGTGGGTGCGGGCTCACTGATAC
GGCTGTGAGCGGCATTGGAGTGTGCGTGGGTCTTCTCGCTACGCTCGGGCCCGCAAGAGGGGTGTGAGAGCGGCTAGGTCCAAGCAGGTGATGTTTGCAG
ACAGAAAAAGTAAACTGTCAAGGAATTCAGAGCATTGGGTACTTGTTATTTGGACCAGTTTGAAGCATCTTTGATTTATTGGACCAACTGGCAACAGAAA
ATGAAAAGTAGTGTGGCACAGATAAAACCTTCTTCTGGTCATGACAGAAGGGAAAACCTTAATTCATATCAGAGGAACTCCTCTCCAGAAGACAGATATG
AAGAACAAGAACGATCCCCCCGGGATAGAGATTACTTTGATTACAGCAGATCAGACTATGAGCATTCAAGAAGAGGACGTTCTTATGATAGTAGCATGGA
GTCACGAAACAGGGACCGAGAAAAACGCAGAGAAAGAGAAAGAGATACGGATCGGAAAAGGTCTCGGAAATCCCCATCTCCTGGGAGGAGAAACCCAGAA
ACATCAGTAACTCAGAGTTCCTCTGCTCAGGATGAACCTGCTACAAAGAAAAAGAAAGATGAGCTGGATCCTCTTCTTACTCGCACTGGTGGAGCATATA
TTCCCCCTGCAAAGCTCAGGATGATGCAGGAACAGATTACAGATAAAAACAGCTTAGCATACCAGAGGATGAGTTGGGAGGCCCTGAAGAAGTCAATTAA
TGGCCTTATCAACAAAGTCAACATTTCCAACATAAGTATTATTATTCAAGAGCTTCTTCAAGAAAATATAGTTAGAGGAAGAGGACTGCTGTCCAGGTCT
GTTTTGCAAGCACAGAGTGCTTCTCCAATCTTCACCCATGTTTATGCAGCATTAGTGGCAATTATCAACTCAAAATTTCCACAAATTGGAGAATTAATCC
TCAAAAGGTTAATTCTTAATTTTCGAAAAGGCTATCGAAGAAATGACAAGCAACTTTGCCTGACTGCTTCAAAATTTGTGGCGCATCTTATTAACCAAAA
TGTGGCACACGAAGTATTATGCTTAGAGATGCTCACTTTGCTCCTGGAAAGACCAACAGATGATAGCGTTGAAGTAGCTATTGGTTTTCTTAAGGAATGT
GGCCTCAAATTAACACAAGTGTCACCAAGAGGAATCAATGCTATATTTGAACGCCTTCGAAACATTCTGCATGAGTCTGAAATTGACAAAAGAGTTCAAT
ATATGATTGAAGTGATGTTTGCTGTACGGAAAGATGGATTCAAGGACCACCCCATTATCCTAGAAGGTCTTGATTTGGTGGAAGAAGATGATCAATTCAC
TCATATGCTCCCTCTGGAGGATGACTATAATCCAGAAGATGTTCTTAATGTTTTCAAGATGGATCCTAATTTTATGGAGAATGAAGAGAAGTACAAAGCT
ATTAAGAAAGAAATTCTTGATGAGGGAGATACTGACTCGAACACAGACCAGGATGCTGGGAGTAGTGAAGAGGACGAGGAAGAAGAAGAGGAAGAGGGAG
AAGAAGATGAAGAAGGACAAAAAGTAACTATTCATGACAAAACAGAAATTAACCTGGTCTCATTTCGTCGTACAATTTATCTTGCTATTCAGTCAAGTTT
AGATTTTGAAGAATGTGCTCACAAATTGCTGAAAATGGAGTTTCCTGAAAGCCAAACAAAAGAACTCTGCAACATGATACTTGATTGCTGTGCCCAACAG
AGGACATACGAAAAATTTTTTGGCTTATTAGCTGGGCGATTTTGCATGCTAAAGAAAGAGTACATGGAATCCTTTGAAGGTATATTCAAAGAACAGTATG
ATACCATCCATCGCTTGGAAACAAACAAGTTGCGAAATGTTGCTAAGATGTTTGCTCACCTTTTATACACTGATTCACTTCCATGGAGTGTTCTTGAATG
TATAAAACTGAGTGAAGAAACCACTACATCATCCAGTAGAATTTTTGTCAAAATATTTTTCCAGGAACTGTGTGAATACATGGGTCTTCCTAAACTTAAT
GCAAGATTAAAGGATGAAACTCTGCAGCCATTCTTTGAAGGATTATTACCCCGAGATAATCCAAGAAACACTCGGTTTGCCATCAACTTCTTTACTTCTA
TAGGTCTTGGAGGTTTAACGGATGAACTGCGGGAGCATCTCAAAAATACACCAAAGGTCATTGTGGCGCAGAAACCAGATGTTGAGCAAAATAAATCCTC
CCCATCCTCTTCCTCTTCAGCGTCCTCCTCTTCAGAGTCTGACTCATCCGACTCTGATTCTGACAGCAGTGATAGCAGTTCAGAGTCTTCCAGTGAAGAG
AGCGACTCTTCATCCATCAGTAGTCATAGCTCTGCCTCAGCTAATGATGTAAGAAAGAAGGGACATGGGAAGACCAGAAGTAAAGAGGTAGATAAATTGA
TCAGAAACCAGCAAACAAATGATAGGAAACAAAAAGAAAGAAGACAAGAACACGGGCACCAGGAAACAAGGACTGAGAGAGAAAGAAGGTCAGAAAAACA
CAGAGATCAAAATTCAAGTGGTTCAAATTGGAGAGATCCTATAACAAAGTACACATCAGACAAAGATGTTCCTTCTGAACGAAATAACTACAGTAGAGTT
GCGAATGACAGAGACCAAGAAATGCATATAGATTTGGAAAATAAGCATGGTGATCCCAAAAAGAAGAGAGGAGAGAGAAGAAATTCTTTTTCTGAAAATG
AGAAGCATACACACCGAATTAAAGACAGTGAAAATTTCAGAAGAAAAGATAGATCAAAGTCAAAGGAAATGAATAGAAAGCACTCAGGCTCAAGAAGTGA
TGAAGATAGATATCAAAATGGTGCCGAGAGACGATGGGAAAAATCTAGCAGATACTCTGAACAATCCAGAGAATCAAAGAAAAATCAGGACCGGCGAAGA
GAAAAGTCTCCAGCAAAACAAAAATAATTCTACAAAATGACATAAACTGGACATGCCTTATATTCAGTTGAAACAAATTATTTTTTACTTTGACGAACTT
TATAGAGAATTCTTGTATAAAGTATTGGTTTGTATTTGTAAATTTAAAAAATGTTTTCATTTTAACATGTTTTATAATTGATACATCTCAAGGCCCTACC
CATAAAATTATTTGAAAACTTTCACCAGAAAGGGATGTAAGTCTCGCTTATATTTTGTGAATAAAATGATCAAAAGCTCA

Loop counts:

3 nts: 1
4 nts: 1
8 nts: 1

Tetra-loop variants:

AAUU    1

Single bulge variants:

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