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

GCTCCCGGGTGGCAAGATGGTGGCGCGCAGGAGGAAGTGCGCCGCGCGGGACCCGGAGGACCGTATCCCCAGCCCACTGGGCTACGCAGCTATTCCAATC
AAGTTCTCTGAAAAGCAACAGGCTTCTCACTACCTCTATGTGAGAGCACACGGCGTTCGACAAGGCACCAAGTCCACCTGGCCTCAGAAGAGGACTCTTT
TTGTCCTCAATGTGCCCCCATACTGCACAGAGGAGAGCCTGTCCCGCCTCCTGTCCACCTGTGGCCTCGTCCAGTCTGTAGAGTTGCAGGAGAAGCCGGA
CCTGGCTGAGAGCCCAAAGGAGTCAAGGTCGAAGTTTTTTCATCCCAAGCCAGTTCCGGGTTTCCAGGTAGCCTATGTGGTGTTCCAGAAGCCAAGTGGG
GTGTCAGCGGCCTTGGCCCTGAAGGGCCCCCTGCTGGTGTCCACAGAGAGCCACCCTGTGAAGAGTGGCATTCACAAGTGGATCAGTGACTACGCAGACT
CTGTGCCCGACCCTGAGGCCCTGAGGGTGGAAGTGGACACGTTCATGGAGGCATATGACCAGAAGATCGCTGAGGAAGAAGCTAAGGCCAAGGAGGAGGA
GGGGGTCCCTGACGAGGAGGGCTGGGTGAAGGTGACCCGCCGGGGCCGGCGGCCTGTGCTCCCCCGGACTGAGGCAGCCAGCTTGCGGGTGCTGGAGAGG
GAGAGACGGAAGCGCAGCCGAAAAGAGCTGCTCAACTTCTACGCCTGGCAGCATCGAGAGAGCAAGATGGAGCATCTAGCGCAGCTGCGCAAGAAGTTCG
AGGAGGACAAGCAGAGGATCGAGCTGCTGCGGGCCCAGCGCAAATTCCGACCGTACTGAGCTGTGAGAGCCGCAGTGAATGGCTGGAGGTGCAGGGCCAG
GAGGAGGCGAGGCAGGGCCTGCAGCGGTCTCTGAGAGGCCGAGCTCTGGCCAACGGGCCCCAGGTTGAAGGCCACCGCGTCCAACAGCCCCATCAGAGTC
CACACAGGCCAGGAGGGAAGGACCAGGCCACCCCTCGGGTCTTGTGCTTCAGCAGTCCTGGGGACCCAGGCGTGCCGAGAGGAGGACTTGTCCTTCCTGC
TTCTTGCCTCCACACCCTCCTCTCCAGGACCCTGGATGAATCCGTTCTGTGCTTCCTTTTCCCTCAATGCAAAAGCCCTTGCTGGCAACGAAAAAGCCTC
AAAAGCAGTGAGAATACAAGAACCTTTTATTTTCCATCCAGTTGGGCAGCAGGGAAAGGCTAGGTGGGCCCAGCCCGCCCTTCCTTCCTCCAGCTGGCTG
GAGATTATTAGCCAGGAGACAGCAGCCCTGGAACCCAGACTCTGTCTCCCCCTTGAGGTCACAGATGTTGAAGTTGGAATCTCGCTCCTTCCCCTGACTA
CCATCCTAGGCTGGGCCTCAAGACTAGTGAGGCCTGTCCCCACCATCCCTGGCCTTGTTGTGGGGCTCAGGAACTCAGAGTCCCAGTGTTGAGTCTGGGA
GCACTAGGTCTTCATAGTTCCAGGCCCAGAGCTACAGCTGGGCTGGGAGCGTGTGTGTGCACTGTAAGAAGGAGCTGATGATACTGGCCACGTGCTGGGG
TTCGCTCATGTGGACACAGTGATTGCCTGGGACTTCCACAAACTGGAACCGCTGGAGAGGGGAGGGGGTGGGTAGTGAGATGTGGCCAGAGGAGCCTAGG
GAGCTCCATGGGCCCCGGGGTCAGGGCCCTCCCACAGCATTCCAGCTCCCTGCAGGTCAGGAGCGCCTCCCACAGTGAGTTTCCCCCACACTCGGCTCCT
TGGAGCCCCGACAGTCCATAGCACCCCAGGAGATGTCTAACCTTAGGGACTTGGAGGCCTCCCAGGGGTCTAGGCCAGCTGAGTTGTGAAGTTGCATGGC
AGGGACAGGGCAGGGCCGAGGCCAGGGTTGCTGTGATTGTATCCGAAGTAGTCCTCGTGAGAAAAGATAATGAGATGACGTGAGCAGCCTGCAGACTTGT
GTCTGCCTTCAAGAAGCCAGACAGGAAGGCCCTGCCTGCCTTGGCTCTGACCTGGCGGCCAGCCAGCCAGCCACAGGTGGGCTTCTTCCTTTTGTGGTGA
CAACGCCAAGAAAACTGCAGAGGCCCCAGGGTCAGGTGTAAGTGGGTAGGTGACCATAAAACACCAGGTGCTCCCAGGAACCCGGGCAAAGGCCATCCCC
ACCTACAGCCAGCATGCCCACTGGCGTGATGGGTGCAGAGGGATGAGGCAGCCAGGTGTTCTGCTGTGGTTTGGGAGCCTATAAAGTGAGACTAGGCTGG
GCATGGTGGCTCCCATCTGCAAAACCAGCACTTTGGGAGGCCAAGGTGGGCGGATCGCCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAA
CCCCCATCTCTTAAAAATATAAAAATTAGCTGGGCATGGTGGCAGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCACGAGAGTCGCTTGAACCCG
GGAGGTGGAGGTTACAGTAAGCTGAGATCTTCCCACTGCACTCCAGCCTGAGCGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAGTGTGACTATT
AGCTGGGCATGATGGCATGCGCCTGTAGTGCCACCTACTCAGGTGGCTGAGGTGGGAGGATCATTTGAGCCCAGGAGTTTGAGGCTGCAGTGAGCTATGA
CTGAGCCTGAGCAACAGAATGAGACCCTGTCTCTCAAAAAATGTGGGACTGTCTCTGGCAGTTGGGTCACCTAATTGTGCCTGGCCCCAAGAAGGAGGGG
TGGGTACTTGAGGATGGTAAAGAACCTCCCCACCAAAGGTCTCTGTTTCTTAAATTCTGATTACATGTGTCCCCAGGCCTCTAGGGACTGATCACTGGAG
CATGAGGCCTGATAGATCCTGGTGGTCACTTGTTGGGCCTGGGGGCAGACCAGGGGTCTTTCCCAGTGCATGAGAAGAGATGGGTGAGGTGGGACCAGAG
TGGGCGACAGTGGCTGGACACCAGCTGCCTGAGCCCCGCCTTACCTCTTTGAGGGTGGATTTCATTGTGTCTATCATGAACGACAGGGACTCCTTGTCAG
AGTAATTCTCTCTTGGATCAAAATATCCGTGGACTGCTCTGGAAAGTGAGGAGTTGGGGGTTGTTGGGGTTCATCTTAGAACCGCCTCCCAGCGGTGCCC
CCATCCTGCCCTGGGTTCAGGCCTCTGAGGAGAAACCAAAGCCTGGGCTACCCCAACTCCCACAGCTGGGTCCCTTGACCCTGGGTTGGATTTGAGGCTC
AGTTAATCTCAGCTCACGCTCAGCTGGCACAAGCCAGGCGCAAGCAAGTGCTGAAGGCACAGCCTTGCTGGGGCGCAGGGAGTTCAGGACTTGGTCACAG
TCAGCCCTGAACAGCAGAGCTGGGATCTGAACAGGCGCTGGAGCCCACACTTGCTCTGAGAGAGAATTTATGTCTTCACAATCCTCCCATTGAAAGTCTA
CAATCCTGGCCGGGTATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACGAGGTCAGGAGATGAGACCATCCTGGCTA
ACATGGTGAAACCCTGTCTGTACTAAAAATACAAAAATTAGCCGGGCTTGGTGGTGGGTGCCTGTAGTCCCAGCTACTCCGGAGGCTGAGGCAGGAGAAT
GGCGTGAACCCGGGAGGCGGACCTTGCAGTGAGCTGAGATTGCACCACTACACTCCAGCCTGGGCGACAGAGCCAGACTCCATCTCAAAAAAAAAAAAAA
A

Loop counts:

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

Tetra-loop variants:

UGAA    2
GGAC    1
GAGU    1
AGGA    1
GUGA    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: 1
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