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

GTACCTGTAGCTGCGGCGCTGAGGTCGGAACGTCTGCGTGTGTGCGGGCTGGTTTTGTGGCGGCTGCTGCTAGAGCTGGAGCATTTGCCGGGTTGGTGGC
TCCTGCACATTTTTACAGTTCTCCAGTCCTTCTCTTTCGTCAGTATAAAAGATTAAACTCTACAGAAGAATGCAATCAAGTGATGGCTTTTCCTTTAGAA
TTTGAATATGGAGGCTACAGGAACAGATGAAGTTGACAAGCTAAAAACCAAATTTATATCTGCTTGGAACAACATGAAATATAGTTGGGTGTTGAAAACA
AAGACGTATTTTAGTAGAAATTCTCCTGTATTATTGCTTGGAAAATGTTACCATTTTAAATATGAAGATGAAGATAAAACGTTACCTGCAGAGTCGGGAT
GTACAATAGAGGATCACGTAATTGCAGGAAATGTAGAAGAATTTCGTAAAGATTTCATTTCTAGAATATGGCTGACCTACAGGGAAGAATTCCCTCAAAT
AGAAGGCTCAGCTTTGACAACAGACTGTGGGTGGGGCTGCACATTGAGAACTGGCCAGATGCTCTTGGCTCAAGGACTCATACTACACTTTCTTGGTAGA
GCTTGGACCTGGCCTGATGCTTTGAATATTGAAAATTCAGACTCTGAATCATGGACTTCCCACACTGTCAAAAAATTTACTGCATCATTTGAAGCATCAC
TTTCAGGGGAAAGAGAATTCAAAACCCCAACAATTTCTCTGAAGGAAACAATTGGGAAATATTCTGATGATCATGAAATGCGAAATGAAGTTTATCATAG
GAAAATCATCTCTTGGTTTGGTGATTCCCCCTTGGCTCTTTTTGGCTTACATCAACTAATAGAATATGGAAAGAAGTCTGGGAAAAAAGCAGGAGATTGG
TATGGACCAGCTGTGGTTGCTCACATTTTAAGAAAAGCAGTTGAAGAAGCAAGGCATCCTGATTTACAAGGAATAACTATTTATGTTGCACAAGATTGTA
CAGTTTACAATTCTGATGTAATTGATAAACAGAGTGCTTCCATGACTTCTGATAATGCAGATGACAAAGCTGTTATTATTCTAGTTCCTGTTAGACTTGG
TGGAGAAAGAACCAACACCGACTACTTAGAATTTGTGAAGGGTATTTTAAGCCTGGAATATTGTGTGGGTATTATTGGTGGCAAACCTAAACAGTCATAT
TACTTTGCTGGATTTCAAGATGACAGTTTGATTTACATGGATCCTCATTACTGCCAATCTTTTGTAGATGTCAGCATAAAGGATTTCCCTCTTGAGACAT
TCCACTGCCCTTCTCCCAAAAAGATGTCTTTTCGAAAAATGGATCCCAGCTGTACAATAGGATTTTACTGTCGAAATGTTCAGGACTTCAAACGAGCTTC
TGAAGAAATCACCAAGATGCTGAAATTTTCTTCTAAGGAGAAATATCCCTTATTTACTTTTGTAAATGGTCATTCCAGAGACTATGATTTTACATCTACT
ACAACCAATGAAGAAGACCTTTTTTCAGAGGATGAAAAGAAACAATTAAAAAGATTTAGCACGGAAGAGTTTGTCTTGCTTTAAAGATTAGCACATTTGT
GCTTGATAAGAAGAATTCCATTGAAAGGGGAAAAATGAAGAGAAACAAGTATATCTGAAATGTTTATTTTCACAAATATCTTAATTTTATATGTTCTTTA
AAAAAGAACATTTGAAAATATAACAGTTAAAGATATTTTTCTAAAAGAGAAATGATTTAATGAATCTTGCTTTCTAATAAATAAATTGAGTGATTCTGGT
TGCATTCCTATTTCCCTAAGATCTACTAGTGATAATTCTACCTTAACTGTAAGCCTTTTAGTCTTCAAAGTCTTCCACCTGAGCCCATTGTTCTCATGGA
GGTTTTGTGATATTAACCCTCCCCCAAAGACTGGGATCACCAAATAGTTTCAAAATTCTCAGTTTGTACTGAAGACCAGAAGATCAGAGAAGGAAACTTT
AATGCTGTCTAGCCTCCTGCTATTAATGCAATCAAAGAATACTTTTGCATATGTCTTGATAATTAAATAGTATTTGTTAACTGTGATATGCATACACTTA
TATAAGCAGAATTATGAGTTAAAGTAATACTTAGCAATATGATTTTATAATGGCTCCTCATTATGCTTGCTGTTGAACCTTTTATGAGGAGTGAATATAA
AGTATTGGTTTTCCCTCACAAATTTAAAGATTATGTTATTAATACTATTATAACTGCATCAATCAAGTCAGATAAAGGCAACTATAAAATAGTAGTAGTG
TTTGTTTCCTATCTCAAGGGCGAAATTTTATGGGAACTCAATTTATTATGCAGTTTTTAAGTTTAAAATACCAAGAAAGATGTCACTAGATTCTCTTCTA
TGTGATTTTTGTTTTTTATATAAAGCAGTGTAGTGGTGTTTAGAAGCTGAGGCCACCTGTAAGGCAAATCTGCCTTAAGTGTATTATGTGTTACTTAAAG
GCAAATTTGTGATCTAAAAGTACAAGAGTGATTTTTGAGCTAGGATTATAAAATACATAATAAAGATGTGAGAAGATAAAATGCTTTTGTTTTGGTTTTA
ATGTTGGGATTATTTTAATCCTTTCATTTGAAAAATCAGTGTCTCAAATGAATTCTGTTCATTTATAATAAATGCATATATTGCTCTGAAAACAATATTA
ATTTTTTTAAGTGGAGCTTTCATGTTTCAGTGTAGAAACGTGACTTATAAAGACATAAAATTGTGTATCATCTAAAGTCATTGATCTCTTCCATCAGAAA
ACCTGTTTGTTTAGAGTTGCATGTAAAGCTGAAAGAGAGGGTGGGCGGATTGTTTTAGTATACCTGATGAGAAAAATCAGGTTTGACATTTCTCAGTGAA
GATTACTTACTGAGTTGAAATAAATAGTCTGAAATCTA

Loop counts:

3 nts: 1
4 nts: 3

Tetra-loop variants:

AUUU    1
AAUA    1
UUUU    1

Single bulge variants:

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