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

GGGCTCTCGCCGTGGCGGGAAAACGGCGGCCGCGGCGTCTCCTCCGGGACGCTGAGGGGCCCGAGGAGACCGTGAGGCTCTGGCCTGCAGCTCGCGCCGC
CATGGACGCTGCCGAGGTCGAATTCCTCGCCGAGAAGGAGCTGGTTACCATTATCCCCAACTTCAGTCTGGACAAGATCTACCTCATCGGGGGGGACCTG
GGGCCTTTTAACCCTGGTTTACCCGTGGAAGTGCCCCTGTGGCTGGCGATTAACCTGAAACAAAGACAGAAATGTCGCCTGCTCCCTCCAGAGTGGATGG
ATGTAGAAAAGTTGGAGAAGATGAGGGATCATGAACGAAAGGAAGAAACTTTTACCCCAATGCCCAGCCCTTACTACATGGAACTTACGAAGCTCCTGTT
AAATCATGCTTCAGACAACATCCCGAAGGCAGACGAAATCCGGACCCTGGTCAAGGATATGTGGGACACTCGTATAGCCAAACTCCGAGTGTCTGCTGAC
AGCTTTGTGAGACAGCAGGAGGCACATGCCAAGCTGGATAACTTGACCTTGATGGAGATCAACACCAGCGGGACTTTCCTCACACAAGCGCTCAACCACA
TGTACAAACTCCGCACGAACCTCCAGCCTCTGGAGAGTACTCAGTCTCAGGACTTCTAGAGAAAGGCCTGGTGCAGGCGGCTTGCTGGGGGATGTGAGCG
CTCAGGACGTGATGAGGTACTCGTGGTTCTGGAGCTCTAGAAACACTTCTGATGCATGAAAAATGTGTGATGGTGCAAGGAATGGATTCAGGATGTTGTT
GGAGAAACAAGTTTGTGATTAGTCCTTAAAACTTAGCTCCCTGGGACATTCTTCAATTCCACATCTGTTTCTAGAAACCAGCCCTTTTTCCCCCCACTTT
TGAGAAATAAAAAAGCCTTAGGTAAATAAGTCATTCTCCCTAGCAGAGCCACTTGGGTCTCCTGCATGGAAGCCATCACACTTGGGCAGGTGTTCAGTGA
CTGGTAGGTGTAGATACAGCAGGAGTGGCCATGTGGTCCACGGCTTTTTACCCCTTCTTGATCCTGATTTCTTGGGCTGAATTTAGACTCTCTCACAGAG
GTGGCTCACAGAGAAGGATGGCAGATGGTGCAGCCAACAATGCTGACCGGTGCTTATCCTCTAAGCCCTGATCCACAATAAAAATGGACCCAACTCAGCT
CTGACTCTCTAGGTTTTTGTGCTGCGTAACTACCAAGTAAAAGGACTGAGCCTGTGGCTGAGATGACTCAGTCAACGAAACTGAGGCACACGGCAGTTAA
GTGGAAACTGCAGACCAACACCTGGGGTGTCTCCTTCTCTTGGCTACTTCTAGCTCAGGTTTAATGGGTTGCTTATCAAGAGGAGAGTCAGGAAAAAAAC
GAATCCAATGTATTGAGCATGAGTGACAATGTATTGAGCATGAGTGACAATGCTAGAAGAAAAGTCACTTTCAGTGCTGCTCTTGATGGATTTGGGGAAG
GATTCTTTGTTGTAGGTAACAGTGGGCTCAGGGGAAATTATTTTTTTCCTAAGAGAAAATTACTTTATTCGTAGCATTTTGGAAATGTTAGGACCTTTAC
AGAAATTACATTACCTTGAGAGGTGAAATGATCGTCCAGCATCATGCAATGGATAGAAGGTTCTGTAATCAGCTTTAAAAAAAACTTTAATTTTTGGCCG
GGCACATTGGCTTGGCTCATGCATGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACAAGGCCAGGAGATTGAGACTATCCTGGCTAACATGG
TGAAACCCCGTCTCTATTAAAAATACAAAAAAAAAAAAATTTGCCAGGTGTGGTGGCACACGCCTATAGTCGCAGCTACTCGGGAGGCTGAGGCAGGAGA
ATCGCTTGAACCCGAGAGGCGGAGGTTGTAGTGAGCCAAGATTGCACCACTGTACTCCTGCCTGGGCAACGAGAGCAAGACTCTGTCTCAAACAAAAAAA
ATTTTAACTTTTTTTTTAGACAGGGTCTCGTTCTGTCATCCAGGCTGCAGTAGAGTGGCGTGATTATAGCTCACTGCAGCCTCGAACTCCTGGGTTCACA
CAGTTCTCCCACCACAGCCTCCCAAAGCACTGGGATTGCAAGCATGAGCCGCCATGCCTGGCCAGCCTATTTTTGGCTGGACACCAGTGGGCCAAAAGCA
GTGGGGTGCTGTCTGGGGAGCTCTGAGAATGCGCATGTGTGACAGGCTGAGCCTAAAGACTTATCACCCAGCATCTGCCCTCCAGTGTCTAGCATGCTGC
ACACTATCACTCCATGTTGCTGCCCACGTGTCCCCGCCAGGCAGGTTTTGGTGGTTATTTGGACACTGAAGGGTCAGACCTGGAAGACTGGGACCAAAAG
ATGAGGTCTCCATAATTTAAGGTGCTGTTCAGACTTGGTTCAGCTCATAGGACTTGTTCTTTCATCTCAGCCTTCCTTGGAATCCTCCTGCTTTCATCTG
GGGATCTTTTAGAATGAAACCACTTGTTATTGTGGAGGGCAAGGGGTCCTAATGCCCTCCTCTTAGAGCCTGAGCCAGTGGAGGCAGCTCCGTCTGCGGA
GATGTATAGTTATTGAGCTTTTCTTTGTTTGGCTTTGTTTTATATCATAAAAAAGATTTTCCTCTTAACATAA

Loop counts:

3 nts: 2
4 nts: 4
5 nts: 4
9 nts: 1

Tetra-loop variants:

CUCC    1
GUGA    1
GAUG    1
AGGU    1

Single bulge variants:

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

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