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

CCCCAACCCTCCCTTTCCTGAATTCCCCCTCCTCCTCGCTCACCTTAAAACCATCGTGCATCACCATGGCGAGTTGCTCCTTCACTCGCGACCAAGCGAC
AAGAAGACTAAGAGGTGCAGCAGCGGCGGCAGCGGCAGCTCTAGCAGCAGTGGTGACCACCCCGCTTCTTTCCTCGGGAACCCCGACCGCACTCATTGGG
ACCGGGTCGTCTTGTCCGGGAGCCATGTGGCTCTCCACGGCCACTGGCTCCCGGTCAGACTCCGAGTCCGAAGAGGAGGACCTGCCCGTCGGGGAGGAAG
TCTGCAAACGCGGCTACCTGCGGAAACAGAAGCATGGGCACAGGCGCTACTTCGTGCTCAAACTCGAGACTGCTGACGCCCCAGCTCGGCTGGAATACTA
CGAAAATGCCAGGAAGTTCCGGCACAGTGTCCGCGCCGCGGCGGCTGCAGCAGCGGCGGCCGCCTCTGGCGCCGCGATCCCCCCGCTCATTCCACCGCGG
CGCGTGATCACCCTATACCAGTGCTTTTCCGTGAGCCAGCGAGCAGATGCAAGGTACCGACACCTCATTGCTCTTTTCACCCAAGACGAATACTTCGCGA
TGGTGGCCGAGAACGAGTCGGAGCAGGAAAGCTGGTACTTGCTGCTCAGCCGCCTCATCCTCGAGAGCAAGCGCCGCCGCTGCGGCACGCTCGGCGCGCA
GCCGGACGGAGAGCCGGCCGCGCTGGCGGCGGCAGCGGCGGCGGAGCCACCCTTCTATAAAGATGTGTGGCAGGTAATAGTCAAACCCAGGGGGCTGGGG
CACAGAAAAGAGCTGAGCGGCGTGTTCCGGCTGTGTCTAACCGACGAGGAGGTCGTGTTTGTGAGGCTGAACACCGAAGTGGCCAGCGTGGTCGTCCAGC
TCCTGAGCATCCGTCGCTGTGGACACTCGGAGCAGTATTTCTTCTTGGAAGTAGGCAGGTCCACTGTCATCGGTCCGGGAGAGCTCTGGATGCAGGTCGA
TGACTGTGTGGTTGCCCAAAACATGCATGAGCTGTTTTTGGAGAAGATGAGAGCCTTGTGTGCAGACGAATACAGAGCCCGCTGCCGCAGCTACAGCATC
AGCATCGGCGCCCACCTGTTAACCCTGCTGTCCGCTAGGAGGCACCTGGGCTTGGTGCCGCTCGAGCCGGGAGGCTGGCTCAGAAGGTCCCGCTTTGAGC
AGTTTTGCCACCTCAGGGCCATCGGCGACGGGGAAGACGAGATGCTTTTCACCAGGCGCTTCGTAACACCCAGCGAGCCTGTGGCCCACTCCAGGCGAGG
AAGACTGCACCTGCCCAGAGGGCGCAGGTCAAGGAGAGCGGTTTCAGTGCCGGCCAGCTTTTTTCGCCGCTTAGCACCCAGCCCAGCACGTCCCCGGCAC
CCTGCAGAAGCCCCGAACAATGGAGCTCGCCTGTCTTCTGAAGTGTCTGGTTCTGGCTCTGGCAACTTTGGGGAGGAAGGCAATCCCCAGGGCAAAGAAG
ATCAGGAAGGAAGCGGAGGTGACTACATGCCTATGAACAATTGGGGCTCAGGAAATGGCCGGGGCTCAGGAGGTGGCCAGGGCTCAAATGGCCAAGGCTC
CAGTAGCCATAGCTCGGGAGGAAACCAGTGTTCAGGCGAGGGACAGGGATCCCGAGGTGGTCAGGGCTCAAATGGCCAGGGCTCAGGAGGAAACCAGTGC
TCTAGAGATGGCCAGGGCACCGCAGGTGGGCACGGTTCAGGTGGTGGCCAGAGACCTGGAGGTGGGCATGGCTCAGGTGGTGGCCAGGGACCTGGAGATG
GCCATGGCTCAGGTGGTGGCAAGAACTCTGGGGGGGGCAAAGGCTCAGGAAGTGGGAAAGGATCCGATGGTGATGGTGAACGTGGAAAATCTCTGAAGAA
AAGATCCTATTTTGGCAAATTAACTCAAAGCAAGCAACAGCAAATGCCACCACCTCCACCACCTCCTCCTCCACCCCCACCAGCTGGAGGAACTGGTGGA
AAAGGGAAGTCTGGGGGAAGATTCAGACTTTATTTTTGTGTTGACAGAGGAGCCACGAAAGAATGCAAAGAAGCCAAAGAAGTGAAAGATGCAGAGATCC
CAGAAGGTGCAGCTCGAGGTCCCCACAGAGCCAGAGCTTTTGATGAAGATGAGGATGACCCATACGTGCCAATGAGGCCAGGGGTGGCCACCCCTCTTGT
AAGCTCCAGTGATTATATGCCAATGGCTCCTCAAAATGTCTCTGCTTCAAAAAAGCGCCACTCTCGATCCCCTTTTGAAGATTCAAGAGGGTACATGATG
ATGTTTCCCAGAGTGAGCCCACCACCTGCTCCGAGTCCTCCAAAAGCACCTGATACTAATAAAGAGGATGACTCAAAGGACAATGACAGTGAGAGTGACT
ACATGTTTATGGCTCCTGGAGCCGGTGCAATTCCAAAAAACCCCAGAAATCCTCAGGGTGGCTCTTCCTCCAAAAGTTGGAGCTCCTACTTCTCTCTACC
AAACCCTTTTCGGAGCTCACCTTTGGGACAGAATGACAACAGTGAGTATGTGCCAATGTTACCTGGAAAGTTCCTGGGGAGGGGCCTAGACAAAGAAGTC
TCCTATAACTGGGACCCCAAAGATGCAGCTTCAAAGCCTTCAGGTGAGGGATCATTCTCAAAGCCTGGAGATGGGGGATCACCTTCAAAGCCTTCAGATC
ATGAGCCCCCAAAGAATAAAGCTAAGAGACCTAACCGACTTTCTTTTATTACAAAAGGATATAAAATCAAGCCAAAACCACAAAAGCCCACACATGAGCA
GAGAGAAGCTGACAGCTCTAGTGACTACGTCAACATGGACTTCACTAAAAGAGAGAGCAATACACCAGCTCCCTCTACTCAAGGACTACCAGATTCGTGG
GGCATAATTGCTGAACCCAGACAGTCAGCCTTTTCTAATTATGTGAATGTTGAGTTTGGAGTGCCATTTCCAAATCCAGCAAACGACCTCTCAGATCTTT
TAAGAGCTATACCACGTGCCAACCCCTTATCTCTGGACAGTGCTAGGTGGCCACTTCCTCCCCTTCCCCTCAGTGCTACAGGTAGCAATGCTATTGAGGA
AGAGGGTGACTACATTGAAGTAATTTTCAACTCAGCAATGACACCAGCCATGGCTCTTGCTGACAGTGCCATTCGCTATGATGCTGAAACAGGTCGAATC
TATGTGGTCGACCCATTTTCTGAGTGCTGTATGGATATTTCTCTCTCCCCCAGCCGATGTTCTGAACCACCACCTGTAGCTAGGCTGCTGCAGGAAGAAG
AGCAGGAGAGAAGACGCCCACAAAGCCGTTCTCAAAGTTTCTTTGCAGCAGCCAGAGCCGCTGTCTCTGCTTTTCCAACAGACAGCCTCGAGAGAGACCT
TTCCCCATCCTCAGCCCCGGCTGTCGCTTCGGCTGCAGAGCCGACTTTAGCCCTCAGCCAAGTTGTAGCTGCGGCCTCCGCGCTCGCCGCAGCCCCGGGC
ATCGGCGCAGCAGCCGCAGCTGCTGGATTTGACTCCGCCTCTGCCCGCTGGTTTCAACCTGTTGCTAATGCTGCTGATGCCGAAGCAGTAAGGGGAGCCC
AAGACGTTGCCGGTGGCTCGAACCCTGGAGCCCACAACCCATCTGCAAACCTTGCCAGAGGTGATAACCAGGCTGGCGGGGCTGCCGCTGCAGCTGCCGC
TCCGGAACCACCACCTCGCAGTCGCCGGGTGCCAAGACCCCCGGAGAGAGAAGATTCTGACAACGACGACGACACTCACGTGAGAATGGATTTTGCCAGA
CGTGATAATCAGTTCGACTCTCCCAAAAGAGGTCGGTAATTTTAGAATTAATTTCCCTAAAGTGAATGGTCATTGTCTAATGATTCGATGCGCTACAGTC
TACAGTGTTAGGGATACTATTTCATTAA

Loop counts:

3 nts: 1
4 nts: 10
5 nts: 2
6 nts: 11
7 nts: 2
8 nts: 1
9 nts: 1
10 nts: 1

Tetra-loop variants:

AGAG    1
AGAU    1
GAUG    1
CAGG    1
GCCA    1
GCAG    1
CGCA    1
CGCU    1
AUAA    1
AUGA    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 1
U x 0 bulge: 3
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: 2
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: 2
C x U bulge: 0
C x C bulge: 0