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

GATTGGCTCATGGGGACGGCCGCGAGCTTTGGTTGGTCGGCGCGGAGTCACGAGGGCGCCGTCGTCGCCTTTCCACAGGCGATTACTGGGCAGGCTCAGT
CTTTCGCCTCAGTCTCGAGCTCTCGCTGGCCTTCGGGTGTACGTGCTCCGGGATCTTCAGCACCCGCGGCCGCCATCGCCGTCGCTTGGCTTCTTCTGGA
CTCATCTGCGCCACTTGTCCGCTTCACACTCCGCCGCCATCATGGTGAAGCTCGCGAAGGCAGGTAAAAATCAAGGTGACCCCAAGAAAATGGCTCCTCC
TCCAAAGGAGGTAGAAGAAGATAGTGAAGATGAGGAAATGTCAGAAGATGAAGAAGATGATAGCAGTGGAGAAGAGGTCGTCATACCTCAGAAGAAAGGC
AAGAAGGCTGCTGCAACCTCAGCAAAGAAGGTGGTCGTTTCCCCAACAAAAAAGGTTGCAGTTGCCACACCAGCCAAGAAAGCAGCTGTCACTCCAGGCA
AAAAGGCAGCAGCAACACCTGCCAAGAAGACAGTTACACCAGCCAAAGCAGTTACCACACCTGGCAAGAAGGGAGCCACACCAGGCAAAGCATTGGTAGC
AACTCCTGGTAAGAAGGGTGCTGCCATCCCAGCCAAGGGGGCAAAGAATGGCAAGAATGCCAAGAAGGAAGACAGTGATGAAGAGGAGGATGATGACAGT
GAGGAGGATGAGGAGGATGACGAGGACGAGGATGAGGATGAAGATGAAATTGAACCAGCAGCGATGAAAGCAGCAGCTGCTGCCCCTGCCTCAGAGGATG
AGGACGATGAGGATGACGAAGATGATGAGGATGACGATGACGATGAGGAAGATGACTCTGAAGAAGAAGCTATGGAGACTACACCAGCCAAAGGAAAGAA
AGCTGCAAAAGTTGTTCCTGTGAAAGCCAAGAACGTGGCTGAGGATGAAGATGAAGAAGAGGATGATGAGGACGAGGATGACGACGACGACGAAGATGAT
GAAGATGATGATGATGAAGATGATGAGGAGGAGGAAGAAGAGGAGGAGGAAGAGCCTGTCAAAGAAGCACCTGGAAAACGAAAGAAGGAAATGGCCAAAC
AGAAAGCAGCTCCTGAAGCCAAGAAACAGAAAGTGGAAGGCACAGAACCGACTACGGCTTTCAATCTCTTTGTTGGAAACCTAAACTTTAACAAATCTGC
TCCTGAATTAAAAACTGGTATCAGCGATGTTTTTGCTAAAAATGATCTTGCTGTTGTGGATGTCAGAATTGGTATGACTAGGAAATTTGGTTATGTGGAT
TTTGAATCTGCTGAAGACCTGGAGAAAGCGTTGGAACTCACTGGTTTGAAAGTCTTTGGCAATGAAATTAAACTAGAGAAACCAAAAGGAAAAGACAGTA
AGAAAGAGCGAGATGCGAGAACACTTTTGGCTAAAAATCTCCCTTACAAAGTCACTCAGGATGAATTGAAAGAAGTGTTTGAAGATGCTGCGGAGATCAG
ATTAGTCAGCAAGGATGGGAAAAGTAAAGGGATTGCTTATATTGAATTTAAGACAGAAGCTGATGCAGAGAAAACCTTTGAAGAAAAGCAGGGAACAGAG
ATCGATGGGCGATCTATTTCCCTGTACTATACTGGAGAGAAAGGTCAAAATCAAGACTATAGAGGTGGAAAGAATAGCACTTGGAGTGGTGAATCAAAAA
CTCTGGTTTTAAGCAACCTCTCCTACAGTGCAACAGAAGAAACTCTTCAGGAAGTATTTGAGAAAGCAACTTTTATCAAAGTACCCCAGAACCAAAATGG
CAAATCTAAAGGGTATGCATTTATAGAGTTTGCTTCATTCGAAGACGCTAAAGAAGCTTTAAATTCCTGTAATAAAAGGGAAATTGAGGGCAGAGCAATC
AGGCTGGAGTTGCAAGGACCCAGGGGATCACCTAATGCCAGAAGCCAGCCATCCAAAACTCTGTTTGTCAAAGGCCTGTCTGAGGATACCACTGAAGAGA
CATTAAAGGAGTCATTTGACGGCTCCGTTCGGGCAAGGATAGTTACTGACCGGGAAACTGGGTCCTCCAAAGGGTTTGGTTTTGTAGACTTCAACAGTGA
GGAGGATGCCAAAGCTGCCAAGGAGGCCATGGAAGACGGTGAAATTGATGGAAATAAAGTTACCTTGGACTGGGCCAAACCTAAGGGTGAAGGTGGCTTC
GGGGGTCGTGGTGGAGGCAGAGGCGGCTTTGGAGGACGAGGTGGTGGTAGAGGAGGCCGAGGAGGATTTGGTGGCAGAGGCCGGGGAGGCTTTGGAGGGC
GAGGAGGCTTCCGAGGAGGCAGAGGAGGAGGAGGTGACCACAAGCCACAAGGAAAGAAGACGAAGTTTGAATAGCTTCTGTCCCTCTGCTTTCCCTTTTC
CATTTGAAAGAAAGGACTCTGGGGTTTTTACTGTTACCTGATCAATGACAGAGCCTTCTGAGGACATTCCAAGACAGTATACAGTCCTGTGGTCTCCTTG
GAAATCCGTCTAGTTAACATTTCAAGGGCAATACCGTGTTGGTTTTGACTGGATATTCATATAAACTTTTTAAAGAGTTGAGTGATAGAGCTAACCCTTA
TCTGTAAGTTTTGAATTTATATTGTTTCATCCCATGTACAAAACCATTTTTTCCTACAAATAGTTTGGGTTTTGTTGTTGTTTCTTTTTTTTGTTTTGTT
TTTGTTTTTTTTTTTTTTGCGTTCGTGGGGTTGTAAAAGAAAAGAAAGCAGAATGTTTTATCATGGTTTTTGCTTCAGCGGCTTTAGGACAAATTAAAAG
TCAACTCTGGTGCCAGACGTGTTACTTCCTAAAGAGTGTTTCCCCTGGAATGTCACTGGAGAGCATGGCAAAGCCAGCTCTGCCACTTGCTTCACCCATC
CCAATGGAAATGGCTTAGTGCGTGTTTCCAGTATCCCAGCCCTAACTAACTTGGTTGAAATGCTGGTGAGGGGACCTGCTCCTGCAGCCCTGGTGCTGAC
TTGAAGGCTGCTGCAGCTTCTCCTACTTTTAGCAGGTCTGAGGATTATGTCCTGAAGACCACTCTGGAAAGAGGTGCAGGAACAGATTAGTCAGGTTTCC
TAGGACAAGGAAGAGCTTCAGGGAAGAGCAGTGGCTAACTCCTGTAATCCCAACACTTGGGGAGGCCGAGGCAGGCAGATCAACTGAGGTCAGGAGTTGA
AGACCAGCCTGGCCAACATGGTGAAAGCCCATCTCTACTAAAAATACAAAAATTAGCTGGGCATGGTGGTGTACTCCTGTAGTCCCAGCTACTCAGGAGG
CTGAAGCGGGAGAGTCACGTGAACCCGGGAAGCAGAGTGAGCTGAGCACACACTACTATACTCCAGGCTGGGTAACAAAGCGAGACTCCCATCTCCCAAA
AAGCAGTTCTGGAATAGAACTCACGCTAGATGGATAGACCAGTGGACACTTTGGAACCTTGGGGCTGGGGAGGAAACTGCCCATCCAGTAAACCCCCAAA
AAGCCATTTGTTCTGCACTACGTATATTGCTTATTCTTTCTGGTCTTAAGTACTTGCCTCTCAACCTCCCTTTTTAGTAAAAGACAAGGCCACGTGAGAG
GCGGGACTATCAACATTGTGATGAATTTACTTGAAACCCAGTGCCCAAAATCAATGTAGGTAGCCAAGTCCAAAAACCTGTTCTAGTCCAACTAGTGAAA
TCAAACTGTGATACTTGGATAAGCTTAGAAGGAAACGTGAAGAATACGTAGCTGCTTTGGGTTTACTCTGGTTCAGTTGGGCTGTTGAAATCTTAACATC
CTTGGGCTTATCACCTACTGCTTGTCAGCCCTGTTCCATGTCCAGGGGATGGGGGTGGTGACAATCCAGTTCCAAGACCCTCATGCTCTAGAGAGGAAGG
TGGCCAGCCAGGGTTGTAACTACGATGAAAAAGCAGTGGGAGGGTCTCCTATGAGGCAAGCCTAAGGACAAAAAGGAAGGCCTTGCAGCCTGTATTCTGG
ATAAGGAATTAAAAGCTCAGTTAATTGAAGCCCA

Loop counts:

3 nts: 2
4 nts: 5
5 nts: 2
6 nts: 2
7 nts: 2

Tetra-loop variants:

UGAA    1
UCUG    1
CCAA    1
UUAA    1
AAAG    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: 1
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: 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