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

GCGAGAGCCCATCTAAAAAAAAAAAAAAAAGAAATTAGAAACAGGGTCTTTGCAGATGTGATTAAATTAAGCATCTTGAGATGGGGGCATTATCCTGGAT
TATTTAGGTGGGCCCTGAATGCCATCTCAAGAGTCCTTATAAGAGAGAGACAGAGGGAGACTAGACACGCAGAGAGAGGAGAAGGCCACGTGAAGACAGA
GCTGAGGATGCTGGCATTGAAGATAAAGCGATGCAGCCACAAGCCAGGGAGTGTCAGCAGAAGCTGGAGGAGGCAAGAAACGTGTTCCTCCCGGGGCCTG
CAGACCCCTTGGTCTCACCCTGGTGACACTGACTTTGGACTTCTGGCCTCCAGAGCTGTAAGATTCTAAGCCACCAAATATATGGTGATTTGTTACGGCA
GCCGAGAGAAACTAATAGGAGAGTGGTTAGTGGTTCACGCTACACCCTGGTCTACACCGGAAGCCTCTCTCCCTGGCACATGATGGTGTCCCCAGGATCC
AGCTCAGAGCCAGGCACACAGTGGGGCCCAGGAGAGACAAAAATGATGTGCAGAAGCAAATGGGTGGGGTTTGCCACCCACCTCCCTTACCTCCCTTGTC
TGTTTAGCAAAGAGGTCTTTCATGCTGGTGTTTTCCAAATTAGGTTGTGACCATGTGTGATCATGACATCCAGGCAGAGGGCTGGCATTTTTCCGAAAAA
GGGTAGAAAATGTCAGAGTATGGTGTGTGTGTAGGCAGGGTCAGTATTGGTCACTGACCCTTACACTGCAGTGGCATTTGTGAAATAGGTCAGGGTCACT
GGTCACGTTGTCTAAGGTGTTATCCGAGCTCGTTTCACAACCAAGAGAATTAAAGAGCATAGACCACCCAAAAGGTGAGGTTGGAGCGAAAGTTTAATAA
GCAAAAGAAGAAAGCTCTCCACAGAGGAGAGGGAAGCCCAAGCGGGTTGCCATTTTTACAGTTGATTCCAAAAGCTTTTTTTTTAAAAAATTATTTATTT
ATTTATTTTTTATTATTATACTTTAAGTTTTAGGATACATGTGCACAACGTACAGGTTTGTTACATGTGTTTATATGTGCCATGTTGGTGTGCTGCACCC
AGTAACTCGTCCTTTAGCATTAGGTATATCTCCTAATGCTATCCCTCCCCCCTCCCCCCACCCCACGACAGTCCCCGGTGTGTGATGTTCCCCTTCCTGT
GTCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGTTGTTTGGTTTTCTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAG
CTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTGTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATC
ATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTACTATTGTGAATAGTGCCGCAATAAACATATGTGTGCATGTGTCTTTATAGCAGCATGATTTATAAT
CCTTTGGGTATATACCCAGTAATAGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCACCACACCGACTTCCACAATGGTTGAAC
TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTTTTTCTCCACATCCTCTCCAGCACCTGTTCTTTCCTGACTTTTTAATGATCGCCGTTCTAACT
GGTGTGAGACGGTATCTCATTGTGATTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTC
TTTTGAGAAGTGTCTATTCATATCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTACATTTGTTTGAGTTCATTGTAGATTCTGGATATT
AGCCATTTGTCAGATGAGTAGGCTGCAAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTTAAACTAAAGAGCTTCTGCACAGCAAAAG
ACACCAAAAGCTTTTATAAGAAACTCCTTTCATCTCTGTAGCTGTTTGAGTATCTTATCTGTAAAGCTATCTGCATAACTCTCCGTTATCTATGTAGTTG
TGGGTACGTCTTTAGGCAAGCACAAAGCTCCGCTTCTCTTGTTTCTGTAACCGTGGGTTTGTTTTAGGTAAGCTCCGCCCCTCCCCGTGCAAGTTCCCAC
AGAGACCACCATGTACGTGCCTGAAAAGGGGAGGGAACTTTTCCTGGGAGCCTGTCAGTCACGCAAAGAACAAAAGGCTTCTGTGCTGGGCAGCTTGAGT
TTTCCCCAGGCTGCTCTATTGTTGCCTGTAGCTGTGATTTTTCAGGCAGGCTGCTCCTCTGAGGACCACCCTTAACTGTCTACCTAACTGGTTTTTCCTT
TTCTTCTCCTCATTTGTATTTATGTATCAGTGTATTATGTATTTATATACACTTGGAGATACAGTAAAATGTACCTCTCACTGTGGGTTACCATAAATAC
TGTAAATTTGAGAAACACTCTTTCAGGCCTGAGAGGAGCAGTGACAACAGTAGGGATGATCAAGTCAGATGTCCCTGGTACCCAGGAATGGCTGGATGAG
AGAAGGAGACAGGGTGACCTGCCCCTGCCTACAAACTCTAACCCAGTTCTGTCCCTGGAGCTGTGTGACCCCGGACAAGGCCCTGCCCCTTTCCAGGCTG
TCGTTGTCCTCATCCAGCCTGGGAGAGGGTTGGCGCTGAGGCCCCCACCTTCTTGCCTGTTTCCTCCTGACCCCACCCCTTCCCCTCCTGCTGGGCAGAT
CCGAGTGAAGCCTGACAGGACCGGTGTGGTCACGGATGGTGTGAAGCACTCCATGAACCCCTTCTGTGAGATCGCGGTGGAGGAGGCTGTGCGGCTCAAG
GAGAAGAAGCTGGTGAAGGAGGTCATCGCCGTCAGCTGTGGGCCTGCACAGTGCCAGGAGACGATTCGTACCGCCCTGGCCATGGGTGCAGACCGAGGTA
TCCACGTGGAGGTGCCCCCAGCAGAAGCAGAACGCTTGGGTCCCCTGCAGGTGGCTCGGGTCCTGGCCAAGCTGGCAGAGAAGGAGAAGGTGGACCTGGT
GCTGCTGGGCAAACAGGCCATCGATGATGACTGTAACCAGACAGGGCAGATGACAGCTGGATTTCTTGACTGGCCACAGGGCACATTCGCCTCCCAGGTG
ACGCTGGAGGGGGACAAGTTGAAAGTGGAGCGGGAGATCGATGGGGGCCTGGAGACCCTGCGCCTGAAGCTGCCAGCTGTGGTGACAGCTGACCTGAGGC
TCAACGAGCCCCGCTACGCCACGCTGCCCAACATCATGAAAGCCAAGAAGAAGAAGATCGAGGTGATCAAGCCTGGGGACCTGGGTGTGGACCTGACCTC
CAAGCTCTCTGTGATCAGTGTGGAGGACCCGCCCCAGCGCACGGCCGGCGTCAAGGTGGAGACCACTGAGGACCTGGTGGCCAAGCTGAAGGAGATTGGG
CGGATTTGAGCCCCTCCCAGAGATGGCAATAAAACTGACTCTCAACATCTA

Loop counts:

3 nts: 1
4 nts: 1

Tetra-loop variants:

GGAC    1

Single bulge variants:

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