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

TACGGCCGTCGTGCCGCTCGTGTCAGTCAACATGGAGGCAGAGGAATCGGAGAAGGCCGCAACGGAGCAAGAGCCGCTGGAAGGGACAGAACAGACACTA
GATGCGGAGGAGGAGCAGGAGGAATCCGAAGAAGCGGCCTGTGGCAGCAAGAAACGGGTAGTGCCAGGTATTGTGTACCTGGGCCATATCCCGCCGCGCT
TCCGGCCCCTGCACGTCCGCAACCTTCTCAGCGCCTATGGCGAGGTCGGACGCGTCTTCTTTCAGGCTGAGGACCGGTTCGTGAGACGCAAGAAGAAGGC
AGCAGCAGCTGCCGGAGGAAAAAAGCGGTCCTACACCAAGGACTACACCGAGGGATGGGTGGAGTTCCGTGACAAGCGCATAGCCAAGCGCGTGGCGGCC
AGTCTACACAACACGCCTATGGGTGCCCGCAGGCGCAGCCCCTTCCGTTATGATCTTTGGAACCTCAAGTACTTGCACCGTTTCACCTGGTCCCACCTCA
GCGAGCACCTCGCCTTTGAGCGCCAGGTGCGCAGGCAGCGCTTGAGAGCGGAGGTTGCTCAAGCCAAGCGTGAGACCGACTTCTATCTTCAAAGTGTGGA
ACGGGGACAACGCTTTCTTGCGGCCGATGGGGACCCTGCTCGCCCAGATGGCTCCTGGACATTTGCCCAGCGTCCTACTGAGCAGGAACTGAGGGCCCGT
AAAGCAGCACGGCCAGGGGGACGTGAACGGGCTCGCCTGGCAACTGCCCAGGACAAGGCCCGCTCCAACAAAGGGCTCCTGGCCAGGATCTTTGGAGCCC
CGCCACCCTCAGAGAGCATGGAGGGACCTTCCCTTGTCAGGGACTCCTGAGGGCCTGGGTGGCCCCTTCCATTTCCTGGCCCTGCTCTGCTTCCTGTCTA
CCTCATACTAGAATGATCGTGACTACCCGGGCAGACATTTTACTGTGTTTCTCAGACCAAGTGTCTACTGATGGCCCAAACATGGAGTTTTGTGGGCTTC
CACTGTCCCCACTCCGAACTCCTGTATGTGCCTGGCTGAGTCACCTAATTCATACTGTCATACTAGCATAATTATGACTATTGCATATGCTTGTTTTGTT
TGACTCTTGGCTGCCTACGTCTGTAGGGTCCCCTGAAAATCCCACTTCCTGCCCCCAGAAAGGGCCTTTATTTCCAACTAGGAGGATAATGCCTAGTCCA
GGCAATCTTTCTCTGTTTAGCAGTCACAGGTGAGGGTGGTATTAGCATCTTTTTTATGTAGAAAAAATTGAGTTAATGGGGTGGACTGGGTTGGGAAGAA
ATACATTTCCTAATGTATTTATAGAAAATAAAAATATTTTTATGTGCCTTTTTATTTTTGTTGGTGGGGAGGTCATTGGACAAGTTCCAACTTTCATCTT
GTGTTCCCTTCACCTTCATATCCTGATCTTAGAGCCCCCCTCCCCCTGCCACCCACCTTACTGTTTAACCTGGATTTTTTTTTCTATTTAATTTTTGTCT
AATATCTTAGCCCAGTTTATCAATCAGTTATCTTAAGTCAGCATTTTCTAAGCCATTGTTTGAGGAAACAGTGACAATAGGTAATAACACATCTTAGTAT
TAAGAGTTTTACAGGCCACTAGTATAAGATAGGCATCGTGGTAGATGCATATAAAGGGTGGAATGGGAGCCATGGCAGGTCATAGAGTCCTCTCAATGGG
AACCTGATTGATGATCACAGTCTTCAGTGGTGAGTCAGTCCTCACCAAGTTTTCCAGATCATTCCTACAAAGTAAACTGGGAGAATAATAAGTCTGAAAG
AGTGTGGAGTGCTCCCACAATTACAAAGAATGCTTCCTGGGTGGAGTGTTGAGTTGGAACCATTGTAAAGGTGGGCAAAGCCTAGTAGAGAACCAGTGCA
CCTCAGGTGCACTTACATATGGTGGGGCTGAGGCAAAGCAGCCCTGTAGGCTTCAAAGAATCAGTGTAAGCCACTAAAAGGAACTGAAAACCTAGGTGTC
ACAATAAACAGTCTACACAGTCTCACGTAGACCAAAATTCTGATCATTTTCCAGGCTGTTGCATGAAGTGATAGAGTATGATTATAATTTCTGTTTGCTT
GTGCTGTTTGTTTTTGTTTTTCATCTGTCAATGTGATGATCTGTGTTTTATAGGGTAGAGTGGATTTGTCTACTTTGGCTGTAAAATACCCTAATCACAT
TATGATCTTGACAGGTGCACTTTACTGGGGAGAATAAAAAGGACCATACGGTAAAGCTGGTATAACATTTCTCACAACCCACATACCTCTTATACTTGGC
ACACAAACTACGTTTCCATTTAGAAACTTTCGTCTTGTTTCTGTTTTTAATTCTTGTGGGTTTGTTTCATGTGAATTGTTTCCTCAGATCATTGATGTCT
TAAAGTGAAACAGAAAAATCCAGAATCAGAATTTGACAGGCTGGCATATTCATTTATTCAGAATTCCAAGTGCCCATTGCTACTTCTGCTAGATAAAGAG
ATACCAAGGTGAAGAAGAAACTTTCCCTCTAGTTGCTAACAGCTTAGAAAGTACAGTAGACATACTGGGGTTTTATTTAAGACTTTCTTGAATGAAGAAA
TAAATTGCATTCCCACGGTGGACAGCGTTAGATAACAGTATGTTCAAGGGCTGGTATTTCAGGGTCCATCTCCAAAACAGTTCTGTACAAAGAGCTCACA
CCTGCGGCCAGGCAAGCTAAGTAAGTCACAGGTGGAGTGAGGAATGAGAATAAATGGGTGGAAGAAAATATCCTAGGAACTTTCATCTTGACTTTAAGCC
CATTGAGTGTAGGAAAATAATTTTTTACATCCACAATTTTGTTTCTATTTAAACAGCACTTGTTTTTTTATATGAAGTAACTCATTTAATCCACAACTAT
ATAATATTGTTATCCCCCCATTAAAACTGAGCTCAGAGAGATGACTCAA

Loop counts:

3 nts: 2
4 nts: 4
5 nts: 1
6 nts: 2
8 nts: 1

Tetra-loop variants:

UCCU    1
AAAA    1
AGCA    1
GCAG    1

Single bulge variants:

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