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

AAGGCGGACAGGAAGGCGTGTGCAAGGCGGGGTCCGGCCCGCGCAGGTCGGGTAAGCGCGTCTAGGGCGCTGCGCGGCGCAGCGAAAATGGCGGCTTCCA
GGTGGGCGCGCAAGGCCGTGGTCCTGCTTTGTGCCTCTGACCTGCTGCTGCTGCTGCTACTGCTACCACCGCCTGGGTCCTGCGCGGCCGAAGGCTCGCC
CGGGACGCCCGACGAGTCTACCCCACCTCCCCGGAAGAAGAAGAAGGATATTCGCGATTACAATGATGCAGACATGGCGCGTCTTCTGGAGCAATGGGAG
AAAGATGATGACATTGAAGAAGGAGATCTTCCAGAGCACAAGAGACCTTCAGCACCTGTCGACTTCTCAAAGATAGACCCAAGCAAGCCTGAAAGCATAT
TGAAAATGACGAAAAAAGGGAAGACTCTCATGATGTTTGTCACTGTATCAGGAAGCCCTACTGAGAAGGAGACAGAGGAAATTACGAGCCTCTGGCAGGG
CAGCCTTTTCAATGCCAACTATGACGTCCAGAGGTTCATTGTGGGATCAGACCGTGCTATCTTCATGCTTCGCGATGGGAGCTACGCCTGGGAGATCAAG
GACTTTTTGGTCGGTCAAGACAGGTGTGCTGATGTAACTCTGGAGGGCCAGGTGTACCCCGGCAAAGGAGGAGGAAGCAAAGAGAAAAATAAAACAAAGC
AAGACAAGGGCAAAAAAAAGAAGGAAGGAGATCTGAAATCTCGGTCTTCCAAGGAAGAAAATCGAGCTGGGAATAAAAGAGAAGACCTGTGATGGGGCAG
CAGTGACGCGCTGTGGGGGGACAGGTGGACGTGGAGAGCTCTTTGCCCAGCTCCTGGGGTGGGAGTGGTCTCAGGCAACTGCACACCGGATGACATTCTA
GTGTCTTCTAGAAAGGGTCTGCCACATGACCAGTTTGTGGTCAAAGAATTACTGCTTAATAGGCTTCAAGTAAGAAGACAGATGTTTTCTAATTAATACT
GGACACTGACAAATTCATGTTTACTATAAAATCTCCTTACATGGAAATGTGACTGTGTTGCTTTTTCCCATTTACACTTGGTGAGTCATCAACTCTACTG
AGATTCCACTCCCCTCCAAGCACCTGCTGTGATTGGGTGGCCTGCTCTGATCAGATAGCAAATTCTGATCAGAGAAGACTTTAAAACTCTTGACTTAATT
GAGTAAACTCTTCATGCCATATACATCATTTTCATTATGTTAAAGGTAAAATATGCTTTGTGAACTCAGATGTCTGTAGCCAGGAAGCCAGGGTGTGTAA
ATCCAAAATCTATGCAGGAAATGCGGAGAATAGAAAATATGTCACTTGAAATCCTAAGTAGTTTTGAATTTCTTTGACTTGAATCTTACTCATCAGTAAG
AGAACTCTTGGTGTCTGTCAGGTTTTATGTGGTCTGTAAAGTTAGGGGTTCTGTTTTGTTTCCTTATTTAGGAAAGAGTACTGCTGGTGTCGAGGGGTTA
TATGTTCCATTTAATGTGACAGTTTTAAAGGATTTAAGTAGGGAATCAGAGTCCTTTGCAGAGTGTGACAGACGACTCAATAACCTCATTTGTTTCTAAA
CATTTTTCTTTGATAAAGTGCCTAAATCTGTGCTTTCGTATAGAGTAACATGATGTGCTACTGTTGATGTCTGATTTTGCCGTTCATGTTAGAGCCTACT
GTGAATAAGAGTTAGAACATTTATATACAGATGTCATTTCTAAGAACTAAAATTCTTTGGGAAAAACCCTCAATTGTGATTTTAATAAATTAAAAGTAGC
ACATTACATGGTTAGAAAATGTCAGTGTTAAAGAATGGTACAAAGTGAAAAGTGTATCCCTCTCTTGCCGCCGGTGGTAGCTTGTCCCAGTGGAAGCTGC
TGTTAACAATTTGTGCCCCCACATCCCCCTCCCTGCCCATCCACCAAAAAAAAGTACATTTACTTATGTAAATGTACTTATGGTGATGTATGTTTGTTTT
GGCCTCACAGCATCTGTTTCCCCTTAATTTGGTAGCTGCTCACATTTCCCTCGAAAGAACCACACCCTCTGCATTCTCAGTTCTCTGCTTTGGATGGGAC
ATTTGCCCTGCAGTCCCCCCACCCTCCAGGCCATGCCCTCTCCAGGGTGAGGCCTGTGTGATCTACCGTACTAGGGTACTAGGCCCTGAAAGAGGCTTTT
CTTGTTCCTCCTGCATCTTGAACCTGGAGCGGGAGCTGTTGTAGGCCCCGCCCTTGGAGAAGAGAACTGTCTGACAGTGGGGAGAGAGCGCCACACCCTG
GTGGCATAAACGAGTCCCTGAATCATGCCGTGGCTGAACCAAGCCCTGTCTGTGGGCTTTTTCTGTTGTACTCAGGGCAGTTTGATGGGGTTACTGTCCT
GCATAGCCATAATGGCCCAGTATAAAGCAGCTGTTTTGATGAGATAATTGCTTTAATTAAGCAAAAGGTAGCAAAGCTTTCACTCCGCCCTGTACCTTCT
GTTTCCACTTAGGAGCCTTCCCATGTCAGAATGTGCAGATCTGTCTCATTGTTTCCTGTGCAGTGTGCCCCCACTTCACCCAGTAGTTTCTGTGTGTCTG
TTATGTACTAGGTACTACAAGGTGCCAGGACGGTGTAGATACAGCCTCTGCTATCGTAAAACTCAATGATTCGGTGGGGGAAGACAAATGTCAGTAATGT
ACAAAGTAAAATGGCAGCTGTTAGAAGTATGAAAGGGGCAGGGTAGGGGGAGGTAGAATCTTCCCTGACCAGGTTAAGAAAACCAGAGGCCTTCTCTGAG
GGCAAGAGGAGGAGAGGAGAAATAGAGTAAGGCAGGCAGAGGAAACAGTCTGAGCTAAGACCCTGTGGCTAGAAGTGGCAGAGGGAGAGGCAGCAGGAAG
GCCAGCGGGGAGGCTGGGGCCCAGTGCAGGCCCAGGTTGGAGGAGCGTAGCACATGGAGTTTGGTAGGAGTTTGGGACGCCCTGGTGGATCTTAATTGTG
ATGGGGTGGGTGTGAAAGGCAGTCCAGGTTGCACTGGTTGCACAGGAGAAGTGATCAGAAGAGGACCCCAGCAGGTGTGAGCCGTGAGCTGGGAGGTGCT
TCAGTAGTGCAGGCCATAGCTGAAGGTGTCCTACATCAGCAGGGTGATGGTGAGGTTTGAACCACTGTTTCACTGCATAGTCCCTGCTGATGGACACTTG
AGTGTTCAGATTTTTTGCTGGTATATTCAGTGCTGCAGTGGACATTTTCATACAAAATATTTCGGTACACTTTTGTTTATATCTGAAAGGTAAATTCCTA
GCAGTAGAATTATTAGAGCAAACGGAATTTAACATTTTGGTGTGTATTGCCAAATTGCCCTCCCAAGTGGTTTAGTCAGCTTACCCTTGCCAACAATAGA
TCTATCCTTGCCAGCCTTGGGCATCACATTTACCAGTTTAATAGATTGTAAAACCATATCTTAATTGGCTACCCTGAAGCCACCATACTGGAGAGGCTGC
GTACAGTGTTTCACGTAGAGAGAGGGATACCCAGGAGGCCCACCTGCTCCAACCCCAGCTGCATGAGTCTTCCCAGCCCAGGCACAGACATGTGGATAAG
ATTTAAACATTTCCAGCCCCAGCCTTCAAGCAATCCTAGTTGACACTGAGGGGAGCCAACATAAGCTGAGCTGAGAAACAGTCTGCCCAGTCTGCAGATT
CATGAGCAAAAGAAATGTTGGGCTGGGTACAGTGGCTCACGCCTGTAATCCCAGTACTTTGGGAGGCCGAGGTGGGTGGATCAGTTGAGGTCAGGAGTTT
GAGACCAGCCTGGCCAACATGGTGAAGCCCTGTCTCTACTAAAAATTAGCCGAGTGTGGTGGTGCGGGCCTGTAATCCCAGCTACTCAGGTGGCTGAGGC
AGGAGAATGGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCAAGATCAGGCCACTGCACTCCAGCCTGGATGACGGGATGAGACTCTGTCTCAAAAAA
ACGAAACAAAAATTTTTTAAGAGAAATGTCATTTGTTTTTGTTTTTGAGACAGGGTCTCACTCTGTTGCCCTCACTAGAGTGCAGTAGGATCACGGCTCA
CTGAAGTCTCTACCTACCGGCTCAATTGATCTTCCCACCACAGCCTCCCAAATAGCTGGGAGAAATGTCCTGTTTTTAATGAATTTGTCTTCCTTTTTGT
CTTGTTTGTTTTAATATCTAGTGATCTAATAAATTTGGATGATATCTTTTGACTATCAATTATG

Loop counts:

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

Tetra-loop variants:

CAUC    1

Single bulge variants:

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