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

CTTTTTCTTCAGCGAGGCGGCCGAGCTGGTTGGTGGCGGCGGTCGTGCGGACGCAAACATGCAGATCTTTGTGAAGACCCTCACTGGCAAAACCATCACC
CTTGAGGTCGAGCCCAGTGACACCATTGAGAATGTCAAAGCCAAAATTCAAGACAAGGAGGGTATCCCACCTGACCAGCAGCGTCTGATATTTGCCGGCA
AACAGCTGGAGGATGGCCGCACTCTCTCAGACTACAACATCCAGAAAGAGTCCACCCTGCACCTGGTGTTGCGCCTGCGAGGTGGCATTATTGAGCCTTC
TCTCCGCCAGCTTGCCCAGAAATACAACTGCGACAAGATGATCTGCCGCAAGTGCTATGCTCGCCTTCACCCTCGTGCTGTCAACTGCCGCAAGAAGAAG
TGTGGTCACACCAACAACCTGCGTCCCAAGAAGAAGGTCAAATAAGGTGGTTCTTTCCTTGAAGGGCAGCCTCCTGCCCAGGCCCCGTGGCCCTGGAGCC
TCAATAAAGTGTCCCTTTCATTGACTGGAGCAGCAATTGGTGTCCTCATGGCTGATCTGTCCAGGGAGGTGGCTGAAGAGTGGGCATCTCCCTTAGGGAC
TCTACTCAGCACTCCATTCTGTGCCACCTGTGGGGTCTTCTGTCCTAGATTCTGTCACATCGGCATTGGTCCCTGCCCTATGCCCCTGACTCTGGATTTG
TCATCTGTAAAACTGGAGTAAAAACCTCAGTCGTGTAATTGGTGGGACTGAGGATCAGTTTTGTCATTGCTGGGATCCTGTCAGGCACTTTGAGGTGTCC
CTCAGGCCTTGGCCCTGAAGTGTCTAGGTGTGTGGAGATGGGTAGAAAATTAGGTACACCCAATGGTGTAGAACGTTGATTCTCAAATTTTTTTATTTTA
TACAAATGGGGTCTCACTATGTTGTCCAGGCTGGTCTTGAACTCCTGGGCTCAAGCCATCCGCCCATCTCAGCCCCTCAAAGTGTTGGGATTACAAGCAA
GAACTGCCATGCCTGACCCAGTTCTCAGTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTTGAGACGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTG
GCGCAGTCTCGGCTTACTACAACCTCTGCCTCCGGGGTTCACATCCTTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCGCCACAACTC
CTGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGGGTTAGCCAGGTTGGTCTCGATCTCCTGACCTTGTGATCCATTCGCCTTGGCCTCCC
AGAATGCTGGTATTACAGGCGTGAGCCAGCACGCCTGGCCCAGTTACTCAGTTTTGAATCTGAGGCCGTGACATCACTCATGGTCTGCAGTCAGTGCTCT
GCCCCTGAGCTGTACCCTCTCCTATGATAATCACTCTTAAGAAGGGCAACCCTTGGTGTTTTCCCCTTAAGGTCACCCAGGCTGGAATGCAGTGGTGTGG
TCATGGCTCCCTGTACCCTGGAACTCAGGCTTGGGTGATCCTCTCTCCTTTGCCTCCGAAGTAGCCAGGACTACAGGTGTGCACCCACCACCACACTCAG
ATAATTGCTTTGGTGTTTTTAAAGCTTGTAATGATCAGTAGGCTGAGGTGGGCAAATCATAAGGTCAAGAGTTTTTTAGATGGGGTGAGCACAGACCAAT
TCCTGTTTTATTTACTGATTTAAAATTTTGAGACAGTCTCACTGTCACCCAGGTTGGGGTGCAGTGGTAGGATCATAGCTTGCTGCAGCCTTGATCTCCC
AGGATCTTGCCTCAGCCTCCCGAGTAGCTGGGACTGCATGCTTGTGCCACCACACTCGGTTAATATTTTGTAGAGATGGGGTCTTGCTATGTTGCCCAGG
CTGGCTTCAAACTCCTGAACTTAAAAGCCTCCTGTTTAGTTTTGGTTTTTTATCACTTTTTTTTTTTTTTTTTGAGATGGAGCCTTGCTCCCATCGTGCA
GGCTGGAGTGCGGTGGCGCAGTCTCGGCTCACTGCAGCTTCTGCCTCTCGGGTTCAAGCGATTCTCCTTTCTCAGCCTCTTGAGTAGCTGGAATTACCAG
TGTGCGCCACCACCACCACGCCTGGCTAGTTTTTCTGTTTTTAGTAGAGACAGGGTTTTGCTATGTTGGCCAGGCTGGTCTTGAACTACTGACCTCTTGT
GATCTACCTGTCTTGGCCTTCCAAAGTGCTAGGATTACAAGCGTAAGCCACAGCGCCTGGCCTTGCTACATTTTTTTTTTTTTTTTTTTTTTTACAGACA
TGGTCTCGCTATGTTGCCCAGAATGGTTTTGCACTGGGTCCAAGCAGTTCTGCCGCAGCCTCCCAAAGTGCTGGGATTACAGGGGTGAGGCACCTTGCTG
GCCCCTGTTTTGATTAGGGTGCAGTGCTGGTGAAGCCGGTGCACGAGGCCAGTGATGCATCCTAATGAGGGGTGGAGTTGGCGGGACTTCCTGGGCCAGT
TTGGGGACTTTCACAAAAGACCCCCATGACTCAGGGTTTTGAGTTCTTAACTGATCGAATGAAGGATTCAAAATTAACCACTCCAAGGGGGGATTGAAGG
AAGAACCACTCTTAATGGACAAAAAGAAAGAAAGGGGAGGGAGTAACAGGGATATGAGCTCTAGCCGCCCAAGCTAGCAATGGCAACCCTTCTGGGTCCC
CTTCCAGCATGTGGAAGCTTTCCTTTCGCTTCATTCAATAAACAGCTGCTGCTCACTCTCCTGGTCCGTGGACTCTTTTTGAACTGTTAACACTCCCCGC
AAAGGTCCGCAGCTTCATTCTTCAAAGTTAGCGAGACCAGGAACC

Loop counts:

4 nts: 2
5 nts: 2
8 nts: 1

Tetra-loop variants:

CCUU    1
CCCU    1

Single bulge variants:

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

1 x 1 internal loop variants:

G x G bulge: 1
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: 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