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

CTGACGCAGGCGCCATTACAGGAGCCGTCTCTCTTGAGGCGACCGTGTCCGCATAAGTTGTCAGTCCCCAGCAGTGTTTGGGAGCCTTAACAGGCTTGCT
AAGTGCCTGAGATTAAAGGCGAAGAGGAAGAAGAGCAAGAAGGGCAACCCGGTGTTTAACACACGGCTTTCAGGCGCTCTCAGGTGGCGCCAAGTTCAGT
TTCGACAGGGATATGCATCCGGGAGAGAATTTTTCAGCCCCCGCCCCCACTGGCATACAGAACAATGGCAGCCCGAGTACTTATAATTGGCAGTGGAGGA
AGGGAACATACGCTGGCCTGGAAACTTGCACAGTCTCATCATGTCAAACAAGTGTTGGTTGCCCCAGGAAACGCAGGCACTGCCTGCTCTGAAAAGATTT
CAAATACCGCCATCTCAATCAGTGACCACACTGCCCTTGCTCAATTCTGCAAAGAGAAGAAAATTGAATTTGTAGTTGTTGGACCAGAAGCACCTCTGGC
TGCTGGGATTGTTGGGAACCTGAGGTCTGCAGGAGTGCAATGCTTTGGCCCAACAGCAGAAGCGGCTCAGTTAGAGTCCAGCAAAAGGTTTGCCAAAGAG
TTTATGGACAGACATGGAATCCCAACCGCACAATGGAAGGCTTTCACCAAACCTGAAGAAGCCTGCAGCTTCATTTTGAGTGCAGACTTCCCTGCTTTGG
TTGTGAAGGCCAGTGGTCTTGCAGCTGGAAAAGGGGTGATTGTTGCAAAGAGCAAAGAAGAGGCCTGCAAAGCTGTACAAGAGATCATGCAGGAGAAAGC
CTTTGGGGCAGCTGGAGAAACAATTGTCATTGAAGAACTTCTTGACGGAGAAGAGGTGTCGTGTCTGTGTTTCACTGATGGCAAGACTGTGGCCCCCATG
CCCCCAGCACAGGACCATAAGCGATTACTGGAGGGAGATGGTGGCCCTAACACAGGGGGAATGGGAGCCTATTGTCCAGCCCCTCAGGTTTCTAATGATC
TATTACTAAAAATTAAAGATACTGTTCTTCAGAGGACAGTGGATGGCATGCAGCAAGAGGGTACTCCATATACAGGTATTCTCTATGCTGGAATAATGCT
GACCAAGAATGGCCCAAAAGTTCTAGAGTTTAATTGCCGTTTTGGTGATCCAGAGTGCCAAGTAATCCTCCCACTTCTTAAAAGTGATCTTTATGAAGTG
ATTCAGTCCACCTTAGATGGACTGCTCTGCACATCTCTGCCTGTTTGGCTAGAAAACCACACCGCCCTAACTGTTGTCATGGCAAGTAAAGGTTATCCTG
GAGACTACACCAAGGGTGTAGAGATAACAGGGTTTCCTGAGGCTCAAGCTCTAGGACTGGAGGTGTTCCATGCAGGCACTGCCCTCAAAAATGGCAAAGT
AGTAACTCATGGGGGTAGAGTTCTTGCAGTCACAGCCATCCGGGAAAATCTCATATCAGCCCTTGAGGAAGCCAAGAAAGGACTAGCTGCTATAAAGTTT
GAGGGAGCAATTTATAGGAAAGACGTCGGCTTTCGTGCCATAGCTTTCCTCCAGCAGCCCAGGAGTTTGACTTACAAGGAATCTGGAGTAGATATCGCAG
CTGGAAATATGCTGGTCAAGAAAATTCAGCCTTTAGCAAAAGCCACTTCCAGATCAGGCTGTAAAGTTGATCTTGGAGGTTTTGCTGGTCTTTTTGATTT
AAAAGCAGCTGGTTTCAAAGATCCCCTTCTGGCCTCTGGAACAGATGGCGTTGGAACTAAACTAAAGATTGCCCAGCTATGCAATAAACATGATACCATT
GGTCAAGATTTGGTAGCAATGTGTGTTAATGATATTCTGGCACAAGGAGCAGAGCCCCTCTTCTTCCTTGATTACTTTTCCTGTGGAAAACTTGACCTCA
GTGTAACTGAAGCTGTTGTTGCTGGAATTGCTAAAGCTTGTGGAAAAGCTGGATGTGCTCTCCTTGGAGGTGAAACAGCAGAAATGCCTGACATGTATCC
CCCTGGAGAGTATGACCTAGCTGGGTTTGCCGTTGGTGCCATGGAGCGAGATCAGAAACTCCCTCACCTGGAAAGAATCACTGAGGGTGATGTTGTTGTT
GGAATAGCTTCATCTGGTCTTCATAGCAATGGATTTAGCCTTGTGAGGAAAATCGTGGCAAAATCTTCCCTCCAGTACTCCTCTCCAGCACCTGATGGTT
GTGGTGACCAGACTTTAGGGGACTTACTTCTCACGCCTACCAGAATCTACAGCCATTCACTGTTACCTGTCCTACGTTCAGGACATGTCAAAGCCTTTGC
CCATATTACTGGTGGAGGATTACTAGAGAACATCCCCAGAGTCCTCCCTGAGAAACTTGGGGTAGATTTAGATGCCCAGACCTGGAGGATCCCCAGGGTC
TTCTCATGGTTGCAGCAGGAAGGACACCTCTCTGAGGAAGAGATGGCCAGAACATTTAACTGTGGGGTTGGCGCTGTCCTTGTGGTATCAAAGGAGCAGA
CAGAGCAGATTCTGAGGGATATCCAGCAGCACAAGGAAGAAGCCTGGGTGATTGGCAGTGTGGTTGCACGAGCTGAAGGTTCCCCACGTGTGAAAGTCAA
GAATCTGATTGAAAGCATGCAAATAAATGGGTCAGTGTTGAAGAATGGCTCCCTGACAAATCATTTCTCTTTTGAAAAAAAAAAGGCCAGAGTGGCTGTC
TTAATATCTGGAACAGGATCGAACCTGCAAGCACTTATAGACAGTACTCGGGAACCAAATAGCTCTGCACAAATTGATATTGTTATCTCCAACAAAGCCG
CAGTAGCTGGGTTAGATAAAGCGGAAAGAGCTGGTATTCCCACTAGAGTAATTAATCATAAACTGTATAAAAATCGTGTAGAATTTGACAGTGCAATTGA
CCTAGTCCTTGAAGAGTTCTCCATAGACATAGTCTGTCTTGCAGGATTCATGAGAATTCTTTCTGGCCCCTTTGTCCAAAAGTGGAATGGAAAAATGCTC
AATATCCACCCATCCTTGCTCCCTTCTTTTAAGGGTTCAAATGCCCATGAGCAAGCCCTGGAAACCGGAGTCACAGTTACTGGGTGCACTGTACACTTTG
TAGCTGAAGATGTGGATGCTGGACAGATTATTTTGCAAGAAGCTGTTCCCGTGAAGAGGGGTGATACTGTCGCAACTCTTTCTGAAAGAGTAAAATTAGC
AGAACATAAAATATTTCCTGCAGCCCTTCAGCTGGTGGCCAGTGGAACTGTACAGCTTGGAGAAAATGGCAAGATCTGTTGGGTTAAAGAGGAATGAAGC
CTTTTAATTCAGAAATGGGGCCAGTTTAGAAAGAATTATTTGCTGTTTGCATGGTGGTTTTTTATCATGGACTTGGCCCAAAAGAAAAACTGCTAAAAGA
CAAAAAAGACCTCACCCTTACTTCATCTATTTTTTTAATAAATAGAGACTCACTAAAAACAAGACTAGTTAGTGCAGCATATCTGAGACA

Loop counts:

6 nts: 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: 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: 0
C x G bulge: 0
C x A bulge: 0
C x U bulge: 0
C x C bulge: 0