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

GGCGCGGCAGGAGGACGAGGCAGGGCGGGCGGGCGCTCTAAGGGTTCTGCTCTGACTCCAGGTTGGGACAGCGTCTTCGCTGCTGCTGGATAGTCGTGTT
TTCGGGGATCGAGGATACTCACCAGAAACCGAAAATGCCGAAACCAATCAATGTCCGAGTTACCACCATGGATGCAGAGCTGGAGTTTGCAATCCAGCCA
AATACAACTGGAAAACAGCTTTTTGATCAGGTGGTAAAGACTATCGGCCTCCGGGAAGTGTGGTACTTTGGCCTCCACTATGTGGATAATAAAGGATTTC
CTACCTGGCTGAAGCTGGATAAGAAGGTGTCTGCCCAGGAGGTCAGGAAGGAGAATCCCCTCCAGTTCAAGTTCCGGGCCAAGTTCTACCCTGAAGATGT
GGCTGAGGAGCTCATCCAGGACATCACCCAGAAACTTTTCTTCCTCCAAGTGAAGGAAGGAATCCTTAGCGATGAGATCTACTGCCCCCCTGAGACTGCC
GTGCTCTTGGGGTCCTACGCTGTGCAGGCCAAGTTTGGGGACTACAACAAAGAAGTGCACAAGTCTGGGTACCTCAGCTCTGAGCGGCTGATCCCTCAAA
GAGTGATGGACCAGCACAAACTTACCAGGGACCAGTGGGAGGACCGGATCCAGGTGTGGCATGCGGAACACCGTGGGATGCTCAAAGATAATGCTATGTT
GGAATACCTGAAGATTGCTCAGGACCTGGAAATGTATGGAATCAACTATTTCGAGATAAAAAACAAGAAAGGAACAGACCTTTGGCTTGGAGTTGATGCC
CTTGGACTGAATATTTATGAGAAAGATGATAAGTTAACCCCAAAGATTGGCTTTCCTTGGAGTGAAATCAGGAACATCTCTTTCAATGACAAAAAGTTTG
TCATTAAACCCATCGACAAGAAGGCACCTGACTTTGTGTTTTATGCCCCACGTCTGAGAATCAACAAGCGGATCCTGCAGCTCTGCATGGGCAACCATGA
GTTGTATATGCGCCGCAGGAAGCCTGACACCATCGAGGTGCAGCAGATGAAGGCCCAGGCCCGGGAGGAGAAGCATCAGAAGCAGCTGGAGCGGCAACAG
CTGGAAACAGAGAAGAAAAGGAGAGAAACCGTGGAGAGAGAGAAAGAGCAGATGATGCGCGAGAAGGAGGAGTTGATGCTGCGGCTGCAGGACTATGAGG
AGAAGACAAAGAAGGCAGAGAGAGAGCTCTCGGAGCAGATTCAGAGGGCCCTGCAGCTGGAGGAGGAGAGGAAGCGGGCACAGGAGGAGGCCGAGCGCCT
AGAGGCTGACCGTATGGCTGCACTGCGGGCTAAGGAGGAGCTGGAGAGACAGGCGGTGGATCAGATAAAGAGCCAGGAGCAGCTGGCTGCGGAGCTTGCA
GAATACACTGCCAAGATTGCCCTCCTGGAAGAGGCGCGGAGGCGCAAGGAGGATGAAGTTGAAGAGTGGCAGCACAGGGCCAAAGAAGCCCAGGATGACC
TGGTGAAGACCAAGGAGGAGCTGCACCTGGTGATGACAGCACCCCCGCCCCCACCACCCCCCGTGTACGAGCCGGTGAGCTACCATGTCCAGGAGAGCTT
GCAGGATGAGGGCGCAGAGCCCACGGGCTACAGCGCGGAGCTGTCTAGTGAGGGCATCCGGGATGACCGCAATGAGGAGAAGCGCATCACTGAGGCAGAG
AAGAACGAGCGTGTGCAGCGGCAGCTGCTGACGCTGAGCAGCGAGCTGTCCCAGGCCCGAGATGAGAATAAGAGGACCCACAATGACATCATCCACAACG
AGAACATGAGGCAAGGCCGGGACAAGTACAAGACGCTGCGGCAGATCCGGCAGGGCAACACCAAGCAGCGCATCGACGAGTTCGAGGCCCTGTAACAGCC
AGGCCAGGACCAAGGGCAGAGGGGTGCTCATAGCGGGCGCTGCCAGCCCCGCCACGCTTGTGTCTTTAGTGCTCCAAGTCTAGGAACTCCCTCAGATCCC
AGTTCCTTTAGAAAGCAGTTACCCAACAGAAACATTCTGGGCTGGGAACCAGGGAGGCGCCCTGGTTTGTTTTCCCCAGTTGTAATAGTGCCAAGCAGGC
CTGATTCTCGCGATTATTCTCGAATCACCTCCTGTGTTGTGCTGGGAGCAGGACTGATTGAATTACGGAAAATGCCTGTAAAGTCTGAGTAAGAAACTTC
ATGCTGGCCTGTGTGATACAAGAGTCAGCATCATTAAAGGAAACGTGGCAGGACTTCCATCTGTGCCATACTTGTTCTGTATTCGAAATGAGCTCAAATT
GATTTTTTAATTTCTATGAAGGATCCATCTTTGTATATTTACATGCTTAGAGGGGTGAAAATTATTTTGGAAATTGAGTCTGAAGCACTCTCGCACACAC
AGTGATTCCCTCCTCCCGTCACTCCACGCAGCTGGCAGAGAGCACAGTGATCACCAGCGTGAGTGGTGGAGGAGGACACTTGGATTTTTTTTTTTGTTTT
TTTTTTTTTTGCTTAACAGTTTTAGAATACATTGTACTTATACACCTTATTAATGATCAGCTATATACTATTTATATACAAGTGATAATACAGATTTGTA
ACATTAGTTTTAAAAAGGGAAAGTTTTGTTCTGTATATTTTGTTACCTTTTACAGAATAAAAGAATTACATATGAAAAACCCTCTAAACCATGGCACTTG
ATGTGATGTGGCAGGAGGGCAGTGGTGGAGCTGGACCTGCCTGCTGCAGTCACGTGTAAACAGGATTATTATTAGTGTTTTATGCATGTAATGGACTATG
CACACTTTTAATTTTGTCAGATTCACACATGCCACTATGAGCTTTCAGACTCCAGCTGTGAAGAGACTCTGTTTGCTTGTGTTTGTTTGTTTGCAGTCTC
TCTCTGCCATGGCCTTGGCAGGCTGCTGGAAGGCAGCTTGTGGAGGCCGTTGGTTCCGCCCACTCATTCCTTCTCGTGCACTGCTTTCTCCTTCACAGCT
AAGATGCCATGTGCAGGTGGATTCCATGCCGCAGACATGAAATAAAAGCTTTGCAAAGGCACGAAGCA

Loop counts:

4 nts: 2
5 nts: 1

Tetra-loop variants:

AUUA    1
AAAG    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: 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: 1
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