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
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:
3 nts: 1
4 nts: 4
5 nts: 2
8 nts: 3
Tetra-loop variants:
CCCU 2
CCUU 1
CCGU 1
Single bulge variants:
G x 0 bulge: 1
A x 0 bulge: 2
U x 0 bulge: 2
C x 0 bulge: 2
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: 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