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

TGGCGAACGGCTGGCCCCGGGCCGCGGGCCTCAGGCAGGTCCGAGGGTGCCCAGGACAGGGTCGGGGCTTGAATGCCTTTGCTTCCGAAAACAGCGGAGC
CGTGGGGCCTCCCCCGCGCCGGCCCTGCCTCCAACCAGCCGCCCAATCCCGGCTCCCATGCGCGTCCACGCCTCCCTATAAGATAAAGCGCGGCCGACGG
GCTCCGAGCGCGGCCCCTGGGTTCGAACACGGCACCCGCACTGCGCGTCATGGTGCAGGCCTGGTATATGGACGACGCCCCGGGCGACCCGCGGCAACCC
CACCGCCCCGACCCCGGCCGCCCAGTGGGCCTGGAGCAGCTGCGGCGGCTCGGGGTGCTCTACTGGAAGCTGGATGCTGACAAATATGAGAATGATCCAG
AATTAGAAAAGATCCGAAGAGAGAGGAACTACTCCTGGATGGACATCATAACCATATGCAAAGATAAACTACCAAATTATGAAGAAAAGATTAAGATGTT
CTACGAGGAGCATTTGCACTTGGACGATGAGATCCGCTACATCCTGGATGGCAGTGGGTACTTCGATGTGAGGGACAAGGAGGACCAGTGGATCCGGATC
TTCATGGAGAAGGGAGACATGGTGACGCTCCCCGCGGGGATCTATCACCGCTTCACGGTGGACGAGAAGAACTACACGAAGGCCATGCGGCTGTTTGTGG
GAGAACCGGTGTGGACAGCGTACAACCGGCCCGCTGACCATTTTGAAGCCCGCGGGCAGTACGTGAAATTTCTGGCACAGACCGCCTAGCAGTGCTGCCT
GGGAACTAACACGTGCCTCGTAAAGGTCCCCAATGTAATGACTGAGCAGAAAATCAATCACTTTCTCTTTGCTTTTAGAGGATAGCCTTGAGGCTAGATT
ATCTTTCCTTTGTAAGATTATTTGATCAGAATATTTTGTAATGAAAGGATCTAGAAAGCAACTTGGAAGTGTAAAGAGTCACCTTCATTTTCTGTAACTC
AATCAAGACTGGTGGGTCCATGGCCCTGTGTTAGTTCATGCATTCAGTTGAGTCCCAAATGAAAGTTTCATCTCCCGAAATGCAGTTCCTTAGATGCCCA
TCTGGACGTGATGCCGCGCCTGCCGTGTAAGAAGGTGCAATCCTAGATAACACAGCTAGCCAGATAGAAGACACTTTTTTCTCCAAAATGATGCCTTGGG
GTGGGGAGTGGTAGGGGGAAGAGCTCCCACCCTAAGGGGCACACACTGAGTTGCTTATGCCACTTCCTTGTTCAAAATAAAGTAACTGCCTTAATCTTAT
ACTCATGGCTTGGAGTTACCTTATATTCAGGTATATGTGATATTTTGCCTGGTTTGTTAAAATTGCCCCATTTAGATTCCTTCTATAATTGTTCTTATAG
ATAAGTAATTTATATATGAGCTGTGTTAGTATTTTTTCAGTGTGAGATCTCTGGATTCTTTCACAATAAAGCTGTTGAATTTTAACAGGAGTATTAGTAC
ATAAATTTTCTACTCAACAATTCCGAGATAGGATTATGCCTAGTTTGTCATATCACAGAAAAACTCCAAGTTAACTTCATGTTTTGGAAGGGCAGGTCGT
TTTTAAAGTATTTCTTTTTTTAACTGGATGAAAAATCTTCATGTTAGGATTAATTTTCTTAATCACCTCCACACTGTACAGAGGAAACTCAAGCCTTAAA
TGTTTAAGTAAACTCTGTCTCAGTTTTAGGATTAAAATACCCACCGGTGGTGTGATGATGCCATATACCGCAGGGCTTGCTTCTGTCAAGTGTGACTCTA
TCTCAGTAATTAAAATAAGTGCTGATCTACTGATTTTTTTTAATGGATTCATTTCTAAATGGGCATTATAAATAGAGCTTGTTCATTTTTAAGAACGAAA
CATTCATATGATAAACTATCGCTTTAAATTGCCTTTCTTGCTTCATATAACTTTTCCCTGTCAGGATCCTTAGTGTTTGAAACTCCTCGTGCGGGGCTGG
CCTCCTGCGGACTCTAGTTTCGCCTCCTTGATGTGGCGCCTGGGATTTCTTCACTTCAGAGCTGTATTTTTACAGGCAAGAGTAAGTTCCTGGGCACAGT
GGCTCATGCCTGTAATCTCAGCTACTCAGGAGGCTAAGGTGGGAGGATTCTTAGAGCCTGGGAGGTCGAGGCTGCAGTGAGCTGTGATTGTGGCCACTGC
ACTCCAGCCTGGGTGACAGAGCGAGACTCTGTCTCAAAAAAGAAGAAAGAGTAAGAGCTGAGGCATATAATAGAATTCTGCTAAAGCACTTAAGGTGAAA
TCACATTTTCTTTTCCCAGGATGTTGCTCACATCTTTCGTTTTTATTGAGGTGTCATTTATATACAATAAAATGTACTCATTTTCAGTGTT

Loop counts:

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

Tetra-loop variants:

GAUG    1
AAUA    1
ACGA    1
UUGA    1

Single bulge variants:

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