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

CGGTGGCCGGTGCGGCGTGTTCGGTGGCGGCTCTGGCCGCTCAGGCGCCTGCGGCTGGGTGAGCGCACGCGAGGCGGCGAGGCGGCAGCGTGTTTCTAGG
TCGTGGCGTCGGGCTTCCGGAGCTTTGGCGGCAGCTAGGGGAGGATGGCGGAGTCTTCGGATAAGCTCTATCGAGTCGAGTACGCCAAGAGCGGGCGCGC
CTCTTGCAAGAAATGCAGCGAGAGCATCCCCAAGGACTCGCTCCGGATGGCCATCATGGTGCAGTCGCCCATGTTTGATGGAAAAGTCCCACACTGGTAC
CACTTCTCCTGCTTCTGGAAGGTGGGCCACTCCATCCGGCACCCTGACGTTGAGGTGGATGGGTTCTCTGAGCTTCGGTGGGATGACCAGCAGAAAGTCA
AGAAGACAGCGGAAGCTGGAGGAGTGACAGGCAAAGGCCAGGATGGAATTGGTAGCAAGGCAGAGAAGACTCTGGGTGACTTTGCAGCAGAGTATGCCAA
GTCCAACAGAAGTACGTGCAAGGGGTGTATGGAGAAGATAGAAAAGGGCCAGGTGCGCCTGTCCAAGAAGATGGTGGACCCGGAGAAGCCACAGCTAGGC
ATGATTGACCGCTGGTACCATCCAGGCTGCTTTGTCAAGAACAGGGAGGAGCTGGGTTTCCGGCCCGAGTACAGTGCGAGTCAGCTCAAGGGCTTCAGCC
TCCTTGCTACAGAGGATAAAGAAGCCCTGAAGAAGCAGCTCCCAGGAGTCAAGAGTGAAGGAAAGAGAAAAGGCGATGAGGTGGATGGAGTGGATGAAGT
GGCGAAGAAGAAATCTAAAAAAGAAAAAGACAAGGATAGTAAGCTTGAAAAAGCCCTAAAGGCTCAGAACGACCTGATCTGGAACATCAAGGACGAGCTA
AAGAAAGTGTGTTCAACTAATGACCTGAAGGAGCTACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCTGATG
GCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGATGCCTATTACTGCACTGGGGACGTCACTGCCTGGAC
CAAGTGTATGGTCAAGACACAGACACCCAACCGGAAGGAGTGGGTAACCCCAAAGGAATTCCGAGAAATCTCTTACCTCAAGAAATTGAAGGTTAAAAAA
CAGGACCGTATATTCCCCCCAGAAACCAGCGCCTCCGTGGCGGCCACGCCTCCGCCCTCCACAGCCTCGGCTCCTGCTGCTGTGAACTCCTCTGCTTCAG
CAGATAAGCCATTATCCAACATGAAGATCCTGACTCTCGGGAAGCTGTCCCGGAACAAGGATGAAGTGAAGGCCATGATTGAGAAACTCGGGGGGAAGTT
GACGGGGACGGCCAACAAGGCTTCCCTGTGCATCAGCACCAAAAAGGAGGTGGAAAAGATGAATAAGAAGATGGAGGAAGTAAAGGAAGCCAACATCCGA
GTTGTGTCTGAGGACTTCCTCCAGGACGTCTCCGCCTCCACCAAGAGCCTTCAGGAGTTGTTCTTAGCGCACATCTTGTCCCCTTGGGGGGCAGAGGTGA
AGGCAGAGCCTGTTGAAGTTGTGGCCCCAAGAGGGAAGTCAGGGGCTGCGCTCTCCAAAAAAAGCAAGGGCCAGGTCAAGGAGGAAGGTATCAACAAATC
TGAAAAGAGAATGAAATTAACTCTTAAAGGAGGAGCAGCTGTGGATCCTGATTCTGGACTGGAACACTCTGCGCATGTCCTGGAGAAAGGTGGGAAGGTC
TTCAGTGCCACCCTTGGCCTGGTGGACATCGTTAAAGGAACCAACTCCTACTACAAGCTGCAGCTTCTGGAGGACGACAAGGAAAACAGGTATTGGATAT
TCAGGTCCTGGGGCCGTGTGGGTACGGTGATCGGTAGCAACAAACTGGAACAGATGCCGTCCAAGGAGGATGCCATTGAGCACTTCATGAAATTATATGA
AGAAAAAACCGGGAACGCTTGGCACTCCAAAAATTTCACGAAGTATCCCAAAAAGTTCTACCCCCTGGAGATTGACTATGGCCAGGATGAAGAGGCAGTG
AAGAAGCTGACAGTAAATCCTGGCACCAAGTCCAAGCTCCCCAAGCCAGTTCAGGACCTCATCAAGATGATCTTTGATGTGGAAAGTATGAAGAAAGCCA
TGGTGGAGTATGAGATCGACCTTCAGAAGATGCCCTTGGGGAAGCTGAGCAAAAGGCAGATCCAGGCCGCATACTCCATCCTCAGTGAGGTCCAGCAGGC
GGTGTCTCAGGGCAGCAGCGACTCTCAGATCCTGGATCTCTCAAATCGCTTTTACACCCTGATCCCCCACGACTTTGGGATGAAGAAGCCTCCGCTCCTG
AACAATGCAGACAGTGTGCAGGCCAAGGTGGAAATGCTTGACAACCTGCTGGACATCGAGGTGGCCTACAGTCTGCTCAGGGGAGGGTCTGATGATAGCA
GCAAGGATCCCATCGATGTCAACTATGAGAAGCTCAAAACTGACATTAAGGTGGTTGACAGAGATTCTGAAGAAGCCGAGATCATCAGGAAGTATGTTAA
GAACACTCATGCAACCACACACAATGCGTATGACTTGGAAGTCATCGATATCTTTAAGATAGAGCGTGAAGGCGAATGCCAGCGTTACAAGCCCTTTAAG
CAGCTTCATAACCGAAGATTGCTGTGGCACGGGTCCAGGACCACCAACTTTGCTGGGATCCTGTCCCAGGGTCTTCGGATAGCCCCGCCTGAAGCGCCCG
TGACAGGCTACATGTTTGGTAAAGGGATCTATTTCGCTGACATGGTCTCCAAGAGTGCCAACTACTGCCATACGTCTCAGGGAGACCCAATAGGCTTAAT
CCTGTTGGGAGAAGTTGCCCTTGGAAACATGTATGAACTGAAGCACGCTTCACATATCAGCAAGTTACCCAAGGGCAAGCACAGTGTCAAAGGTTTGGGC
AAAACTACCCCTGATCCTTCAGCTAACATTAGTCTGGATGGTGTAGACGTTCCTCTTGGGACCGGGATTTCATCTGGTGTGAATGACACCTCTCTACTAT
ATAACGAGTACATTGTCTATGATATTGCTCAGGTAAATCTGAAGTATCTGCTGAAACTGAAATTCAATTTTAAGACCTCCCTGTGGTAATTGGGAGAGGT
AGCCGAGTCACACCCGGTGGCTCTGGTATGAATTCACCCGAAGCGCTTCTGCACCAACTCACCTGGCCGCTAAGTTGCTGATGGGTAGTACCTGTACTAA
ACCACCTCAGAAAGGATTTTACAGAAACGTGTTAAAGGTTTTCTCTAACTTCTCAAGTCCCTTGTTTTGTGTTGTGTCTGTGGGGAGGGGTTGTTTTGGG
GTTGTTTTTGTTTTTTCTTGCCAGGTAGATAAAACTGACATAGAGAAAAGGCTGGAGAGAGATTCTGTTGCATAGACTAGTCCTATGGAAAAAACCAAGC
TTCGTTAGAATGTCTGCCTTACTGGTTTCCCCAGGGAAGGAAAAATACACTTCCACCCTTTTTTCTAAGTGTTCGTCTTTAGTTTTGATTTTGGAAAGAT
GTTAAGCATTTATTTTTAGTTAAAAATAAAAACTAATTTCATACTATTTAGATTTTCTTTTTTATCTTGCACTTATTGTCCCCTTTTTAGTTTTTTTTGT
TTGCCTCTTGTGGTGAGGGGTGTGGGAAGACCAAAGGAAGGAACGCTAACAATTTCTCATACTTAGAAACAAAAAGAGCTTTCCTTCTCCAGGAATACTG
AACATGGGAGCTCTTGAAATATGTAGTATTAAAAGTTGCATTTGAAATTCTTGACTTTCTTATGGGCACTTTTGTCTTCCAAATTAAAACTCTACCACAA
ATATACTTACCCAAGGGCTAATAGTAATACTCGATTAAAAATGCAGATGCCTTCTCTA

Loop counts:

3 nts: 4
4 nts: 7
5 nts: 5
6 nts: 9
7 nts: 1
8 nts: 2
10 nts: 1

Tetra-loop variants:

UGGG    1
UGGA    1
CACG    1
UCUU    1
UAAA    1
AGUU    1
GUUU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 4
U x 0 bulge: 1
C x 0 bulge: 2

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: 2
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