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

AGGCGCGGTTGTGAGTAGTACCGGGAGTGGGGTGATCCCGGGCTAGGGGAGCGCGGCGGCCGCGATCGGGCTTAGTCGGAGCTCCGAAGGGAGTGACTAG
GACACCCGGGTGGGCTACTTTTCTTCCGGTGCTTTTGCTTTTTTTTTCCTTTGGGCTCGGGCTGAGTGTCGCCCACTGAGCAAAGATTCCCTCGTAAAAC
CCAGAGCGACCCTCCCGTCAATTGTTGGGCTCGGGAGTGTCGCGGTGCCCCGAGCGCGCCGGGCGCGGAGGCAAAGGGAGCGGAGCCGGCCGCGGACGGG
GCCCGGAGCTTGCCTGCCTCCCTCGCTCGCCCCAGCGGGTTCGCTCGCGTAGAGCGCAGGGCGCGCGCGATGAAGGCGGTGAGCCCGGTGCGCCCCTCGG
GCCGCAAGGCGCCGTCGGGCTGCGGCGGCGGGGAGCTGGCGCTGCGCTGCCTGGCCGAGCACGGCCACAGCCTGGGTGGCTCCGCAGCCGCGGCGGCGGC
GGCGGCGGCAGCGCGCTGTAAGGCGGCCGAGGCGGCGGCCGACGAGCCGGCGCTGTGCCTGCAGTGCGATATGAACGACTGCTATAGCCGCCTGCGGAGG
CTGGTGCCCACCATCCCGCCCAACAAGAAAGTCAGCAAAGTGGAGATCCTGCAGCACGTTATCGACTACATCCTGGACCTGCAGCTGGCGCTGGAGACGC
ACCCGGCCCTGCTGAGGCAGCCACCACCGCCCGCGCCGCCACACCACCCGGCCGGGACCTGTCCAGCCGCGCCGCCGCGGACCCCGCTCACTGCGCTCAA
CACCGACCCGGCCGGCGCGGTGAACAAGCAGGGCGACAGCATTCTGTGCCGCTGAGCCGCGCTGTCCAGGTGTGCGGCCGCCTGAGCCCGAGCCAGGAGC
ACTAGAGAGGGAGGGGGAAGAGCAGAAGTTAGAGAAAAAAAGCCACCGGAGGAAAGGAAAAAACATCGGCCAACCTAGAAACGTTTTCATTCGTCATTCC
AAGAGAGAGAGAGGAAAGAAAAATACAACTTTCATTCTTTCTTTGCACGTTCATAAACATTCTACATACGTATTCTCTTTTGTCTCTTCATTTATAACTG
CTGTGAATTGTACATTTCTGTGTTTTTTGGAGGTGCAGTTAAACTTTTAAGCTTAAGTGTGACAGGACTGATAAATAGAAGATCAAGAGTAGATCCGACT
TTAGAAGCCTACTTTGTGACCAAGGAGCTCAATTTTTGTTTTGAAGCTTTACTAATCTACCAGAGCATTGTAGATATTTTTTTTTTACATCTATTGTTTA
AAATAGATGATTATAACGGGGCAGAGAACTTTCTTTTCTCTGCAAGAATGTTACATATTGTATAGATAAATGAGTGACATTTCATACCATGTATATATAG
AGATGTTCTATAAGTGTGAGAAAGTATATGCTTTAATAGATACTGTAATTATAAGATATTTTTAATTAAATATTTTTTTGTAAATATTATGTGTGTGTTT
TTTTTTAATCTATGGGAATATTTCTTTTGGAAAATCATTTTTCAGCTCAATTACAGAGCTCTTGATATCTTGAATGTCTTTTCTGTTTGGCCTGGCTCTT
AATTTGCTTTTGTTTTGCCCAGTATAGACTCGGAAGTAACAGTTATAGCTAGTGGTCTTGCATGATTGCATGAGATGTTTAATCACAAATTAAACTTGTT
CTGAGTCCATTCAAATGTGTTTTTTTAAATGTAGATTGAAATCTTTGTATTTGAAGCATACATGTTGAAAATACACCTTATCAGTTTTTAAGTACAGGGT
TTTATAGTGTAATATATACAGAGTAAGTGTTTGTTTTTGTTTTTCAACTGAGGTCAAAATGGATTCTGAATGATTTTGCATATGGGATGAGGAAATGCTT
GGATCCTTAAGGAGTTTACGAAATCTGCTGTTTTATCAAAGTGAAAAAAAATTGCTTATTACTCTTCATTTTACACTAAAGCTTAATGTCACTAAGTTTC
ATGTCTGTACAGATTATTTAAATCATGGAAATGAAAAAAATGTTCTCTGCTTGCTACCAAAGGACAAACTCTTGGAAATGAACACTTTCTGCTTTCCTTC
CTCCAAAGAATTAATAGGCAACAGTGGGAGAAAAAAAAGGCATAATGGCAAATCCTTCAAGCAGGGATAAAAGTCGATCTTCAAACATTAACTTAAGCAG
ACCAAAAATTCTGATGACCGCATCTAGATTATTTTTTTATAAAAATGATTTTCACTATAGCTATGTTACGCTAAGCTACTGTCCAATCTCTTGTGATGTG
TAACTTTTACATGTGAATATTAAAGTAGATTTCTCTGTCTTGTA

Loop counts:

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

Tetra-loop variants:

GGAA    1
UUAU    1
CAGC    1
AGCA    1
GGCG    1
GAAG    1
GCCC    1
CAUU    1
CCAA    1

Single bulge variants:

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

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: 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