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

GCGAGTTGCTGTGCGTTTCTCTGTTGTCTCGGTAGAAGGCCAGAGTCACACACGGTCCTAAGAGCTGGGCACCAGGAAGCGAAGGCTGATCTGAAGAAGA
CACTTGAATCATGGGTGACGTTAAAAATTTTCTGTATGCCTGGTGTGGCAAAAGGAAGATGACCCCATCCTATGAAATTAGAGCAGTGGGGAACAAAAAC
AGGCAGAAATTCATGTGTGAGGTTCAGGTGGAAGGTTATAATTACACTGGCATGGGAAATTCCACCAATAAAAAAGATGCACAAAGCAATGCTGCCAGAG
ACTTTGTTAACTATTTGGTTCGAATAAATGAAATAAAGAGTGAAGAAGTTCCAGCTTTTGGGGTAGCATCTCCGCCCCCACTTACTGATACTCCTGACAC
TACAGCAAATGCTGAAGGAGATTTACCAACAACCATGGGAGGACCTCTTCCTCCACATCTGGCTCTCAAAGCAGAAAATAATTCTGAGGTAGGGGCCTCT
GGCTATGGTGTTCCTGGGCCCACCTGGGACCGAGGAGCCAACTTGAAGGATTACTACTCAAGAAAGGAAGAACAAGAAGTGCAAGCGACTCTAGAATCAG
AAGAAGTGGATTTAAATGCTGGGCTTCATGGAAACTGGACCTTGGAAAATGCTAAAGCTCGTCTAAACCAATATTTTCAGAAAGAAAAGATCCAAGGAGA
ATATAAGTACACCCAAGTGGGTCCTGATCACAACAGGAGCTTTATTGCAGAAATGACCATTTATATCAAGCAGCTGGGCAGAAGGATTTTTGCACGAGAA
CATGGATCAAATAAGAAATTGGCAGCACAGTCCTGTGCCCTGTCACTTGTCAGACAACTGTACCATCTTGGAGTGGTTGAAGCTTACTCCGGACTTACAA
AGAAGAAGGAAGGAGAGACAGTGGAGCCTTACAAAGTAAACCTCTCTCAAGATTTAGAGCATCAGCTGCAAAACATCATTCAAGAGCTAAATCTTGAGAT
TTTGCCCCCGCCTGAAGATCCTTCTGTGCCAGTTGCACTCAACATTGGCAAATTGGCTCAGTTCGAACCATCTCAGCGACAAAACCAAGTGGGTGTGGTT
CCTTGGTCACCTCCACAATCCAACTGGAATCCTTGGACTAGTAGCAACATTGATGAGGGGCCTCTGGCTTTTGCTACTCCAGAGCAAATAAGCATGGACC
TCAAGAATGAATTGATGTACCAGTTGGAACAGGATCATGATTTGCAAGCAATCTTGCAGGAGAGAGAGTTACTGCCTGTGAAGAAATTTGAAAGTGAGAT
TCTGGAAGCAATCAGCCAAAATTCAGTTGTCATTATTAGAGGGGCTACTGGATGTGGGAAAACCACACAGGTTCCCCAGTTCATTCTAGATGACTTTATC
CAGAATGACCGAGCAGCAGAGTGTAACATCGTAGTAACTCAGCCCAGAAGAATCAGTGCGGTTTCTGTGGCAGAGCGAGTTGCATTTGAAAGAGGAGAAG
AGCCTGGAAAAAGCTGTGGCTACAGCGTTCGATTTGAGTCTATACTTCCTCGTCCTCATGCCAGTATAATGTTTTGTACTGTAGGTGTGCTCCTGAGAAA
ATTAGAAGCAGGCATTCGAGGAATCAGTCATGTAATTGTAGATGAAATACATGAAAGAGATATTAATACTGACTTCCTTTTGGTAGTACTGCGTGATGTT
GTTCAGGCTTATCCTGAAGTTCGCATTGTTCTTATGTCTGCTACTATTGATACCAGCATGTTTTGTGAATATTTCTTCAATTGCCCCATCATTGAAGTTT
ATGGGAGGACTTACCCAGTTCAAGAATATTTTCTGGAAGACTGCATTCAGATGACCCACTTTGTTCCTCCACCAAAAGACAAAAAGAAGAAGGATAAGGA
TGATGATGGTGGTGAGGATGATGATGCAAATTGCAACTTGATCTGTGGTGATGAATATGGTCCAGAAACAAGGTTGAGCATGTCTCAATTGAACGAAAAG
GAAACTCCTTTTGAACTCATCGAGGCTCTACTTAAGTACATTGAAACCCTTAATGTTCCTGGAGCTGTGTTGGTTTTTTTGCCTGGCTGGAATCTGATTT
ATACTATGCAGAAGCATTTGGAAATGAATCCACATTTTGGAAGCCATCGGTATCAGATTCTACCCCTGCATTCTCAGATTCCTCGAGAGGAACAGCGCAA
AGTGTTTGATCCAGTACCAGTTGGAGTAACCAAGGTTATTTTGTCCACAAATATTGCTGAAACAAGCATTACCATAAACGATGTTGTTTATGTCATTGAC
TCCTGCAAGCAGAAAGTGAAACTCTTCACTGCTCACAACAATATGACCAACTATGCTACCGTATGGGCATCAAAAACAAACCTTGAGCAACGGAAAGGGC
GAGCTGGCCGAGTACGGCCTGGATTCTGCTTTCACCTGTGCAGCCGAGCTCGTTTTGAGAGACTTGAAACCCACATGACACCAGAGATGTTCCGAACACC
ATTGCATGAAATTGCTCTTAGCATAAAACTTCTGCGTCTAGGAGGAATTGGCCAATTTCTGGCCAAAGCAATTGAACCTCCCCCTTTGGATGCTGTGATT
GAAGCAGAACACACTCTTAGAGAGCTTGATGCATTAGATGCCAATGATGAGTTGACTCCTTTGGGACGAATCCTGGCTAAACTCCCCATTGAGCCTCGTT
TTGGCAAAATGATGATAATGGGGTGTATTTTCTACGTGGGAGATGCTATCTGTACCATTGCTGCTGCTACCTGCTTTCCAGAGCCTTTCATCAATGAAGG
AAAGCGGCTGGGCTATATCCATCGAAATTTTGCTGGAAACAGATTTTCTGATCACGTAGCCCTTTTATCAGTATTCCAAGCCTGGGATGATGCTAGAATG
GGTGGAGAAGAAGCAGAGATACGTTTTTGTGAGCACAAAAGACTTAATATGGCTACACTAAGAATGACTTGGGAAGCCAAAGTTCAGCTCAAAGAGATTT
TGATTAATTCTGGGTTTCCAGAAGATTGTTTGTTGACACAAGTGTTTACTAACACTGGACCAGATAATAATTTGGATGTTGTTATCTCCCTCCTGGCCTT
TGGTGTGTACCCCAATGTATGCTATCATAAGGAAAAGAGGAAGATTCTCACCACTGAAGGGCGTAATGCACTTATCCACAAATCATCTGTTAATTGTCCT
TTTAGTAGCCAAGACATGAAGTACCCATCTCCCTTCTTTGTATTTGGTGAAAAGATTCGAACTCGAGCCATCTCTGCTAAAGGCATGACTTTAGTCACCC
CCCTGCAGTTGCTTCTCTTTGCCTCCAAGAAAGTCCAATCTGATGGGCAGATTGTGCTTGTAGATGACTGGATTAAACTGCAAATATCTCATGAAGCTGC
TGCCTGTATCACTGGTCTCCGGGCAGCCATGGAGGCTTTGGTTGTTGAAGTAACCAAACAACCTGCTATCATCAGCCAGTTGGACCCCGTAAATGAACGT
ATGCTGAACATGATCCGTCAGATCTCTAGACCCTCAGCTGCTGGTATCAACCTTATGATTGGCAGTACACGGTATGGAGATGGTCCACGTCCTCCCAAGA
TGGCCCGATACGACAATGGAAGCGGATATAGAAGGGGAGGTTCTAGTTACAGTGGTGGAGGCTATGGCGGTGGCTATAGCAGTGGAGGCTATGGTAGCGG
AGGCTATGGTGGCAGCGCCAACTCCTTTCGGGCAGGATATGGTGCAGGTGTTGGTGGAGGCTATAGAGGAGTTTCCCGAGGTGGCTTTAGAGGCAACTCT
GGAGGAGACTACAGAGGGCCTAGTGGAGGCTACAGAGGATCTGGGGGATTCCAGCGAGGAGGTGGTAGGGGGGCCTATGGAACTGGCTACTTTGGACAGG
GAAGAGGAGGTGGCGGCTATTAAAACTTGGTTATGTCAGTTCCTGTGTGTAGACAGTAAGGAAAAAAAGGCATGCTATGTGTTACGTGTTTTTTCCAGTA
TGTTTATTTGCCACCAAAAAGTAAATGCATTTTCACCCATTCTGTGGTTCATTGTAGTTTAAGGAAACCAAGCATATAGATGCATTAGTGATTTTGTTTA
TATTATGTAAAATATAACGATCTCTTAAAAATACCACAGTTTGTATTTTTTCTTTAAGGAGTAAAGATTTGCCTTTAAATAACTTGGTATTTTCCTGGCT
TTCGTTTAATACAATAGAAAATAAAGTATTACACCGAATA

Loop counts:

3 nts: 3
4 nts: 14
5 nts: 10
6 nts: 6
7 nts: 1
8 nts: 2

Tetra-loop variants:

AAAU    2
GGCU    1
UGUU    1
AGAA    1
AUGU    1
ACUC    1
UACC    1
AGUA    1
AGCC    1
GGUG    1
GAGA    1
AGAU    1
GUCC    1

Single bulge variants:

G x 0 bulge: 2
A x 0 bulge: 1
U x 0 bulge: 3
C x 0 bulge: 1

1 x 1 internal loop variants:

G x G bulge: 1
G x A bulge: 3
G x U bulge: 0
G x C bulge: 0
A x G bulge: 3
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