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

TCCGCCGGCTCACGTGACCGTCTTTGGGCCGGCGCGAACCATGGCCGGCATGGTGGACTTCCAGGATGAGGAGCAGGTCAAGTCCTTTTTGGAGAACATG
GAGGTGGAGTGCAACTACCACTGCTACCACGAGAAGGACCCGGACGGTTGCTATCGGCTGGTGGACTATTTGGAAGGGATCCGGAAGAATTTTGATGAGG
CTGCCAAGGTGTTGAAGTTTAACTGTGAAGAGAACCAGCACAGTGATAGCTGCTACAAACTGGGGGCCTACTATGTGACTGGAAAAGGTGGTCTGACCCA
GGACCTGAAAGCTGCCGCCAGGTGCTTTTTGATGGCGTGTGAGAAGCCTGGAAAGAAGTCAATAGCAGCATGTCACAACGTTGGCCTCCTGGCACATGAT
GGACAGGTTAATGAGGATGGCCAGCCTGACTTGGGAAAGGCCAGGGACTACTACACAAGGGCCTGTGATGGTGGCTATACTTCCAGTTGCTTCAACCTCA
GTGCCATGTTCCTGCAGGGTGCCCCAGGCTTTCCCAAGGACATGGACCTGGCATGTAAATACTCCATGAAAGCCTGTGACCTGGGTCATATCTGGGCCTG
TGCCAATGCCAGTCGCATGTACAAGCTGGGGGATGGTGTTGATAAGGATGAGGCCAAGGCCGAGGTGCTAAAAAATCGAGCCCAGCAGCTACACAAAGAA
CAGCAGAAAGGTGTCCAACCCTTAACATTTGGGTAATGTGGTCCACCCTCCCTCCCAGGCAACAAACTGCTTGAGGCTGGCAGCTCCTGTTTCTGAAGAC
TGATGCAGCCCTTGAAGGTCAACCTGCTGGAGCAAAAAAACTTGGGACTTGAATTTGTAGCTCCATTTACATGGATCCATTGCCCCAGCTACTGGAGTAT
AGCCTACAATGTTTATTTCAGTCAATATTCCTTTATCTGGGTGTTCTGTACAATGTTTATTACAGTCAATATTCCTTCATCTGGATGTTCTGTGAAGATA
GCCATGTTTATGGGGGTCTTAGTTTTCAAACTCTGGCAACTCTGTGAAAAATAGGAGCAAACTAGAGAGCCCTGGAGATTGGTAGTAGGGAAGGGAGGAT
AGCAGGAAGTTTGAAAAATTAGCAGCCCCGGGGCCTAAAGGAATCAGCTGTCATCATTTTCATCATTATTATTTTGGTTAGGATGGCTTGAAAATCAGAA
CGTATCTTGGTTTACGTAATTGAGGTCTTAAAGAACTAAGAACAGTTAAATAGTCACAACTACCACCCTCTGACTTACATAATCATTGGTGTGGGCTTCG
TTTTGCCTTTAGAGTCACATCTTTCAGTAAATTCACAGAGATCAAGAGGGACGTGCAACATACAGCTTAAAGGCTGTTATGCTTCAGGGTTGCTGAAGAA
GATGAAACATCAGCCTGCCATCGTCTAGAAGAGACATTGGCAGTTAAAAATTAGCACCTCCAGTGTAGTCGCCTGGCACTGCCCATCATGCTGAGGGAGC
AGATTCTTCCCAAGGCAGCTTCAGCTAGGAGTTTGTAAGCAAGGACTTTGTGACACATTTGTCCCCTGGAACTGAGCCTTTTTAACTGTCCCTGTGAATG
AACAATTTTGAGTGACCTACGGTTTGTGTTAATTAGTGTTCTTTCCAGATTCCAGGTACCGTAGAGAGTATGTTCTTTGTGGTGGTTGTGCCTTTTAAGA
ACATTTGTGGCCGGGCACGGTGGCTCACGCCTGTAACCCCAGCACTTTGGGTGGCCAAGGCGGGTGGATCACGAGATCAGGAGATCATGACCATCCTGGC
TAACACGGGGAAACCCCATCTCTACTAAAAAATACAAAAAATTAGCCGGGCGTGGTGGCAGGCGCCTGTAGTCCCAGCTACTGGGGAGGCTGAGGCAGGA
GAATTGCTTGAACCCGGGAGGCGGAGCTTGCAGTGAGCTGAGATTGCGCCACTGCCCTCCAGCCTGGGCGATAGAGTGAGACTCCGTCTCAAAAAAAAAA
AAAAATTTGCTTTTTCTGTTGTCTCCCCAGCTTGTCACCAGGGGGCGAGCTTGCCATTTCCCTGCTGGTAACAATACCATTCTGTCACCATCTACTGTTT
TAGGCTTCCGTTTTGCAGCCGTCCTGAAAGGAAGGCTTGCTGTGTAAATGAAGGCTTGTGAGCACAGCAGCCAGCCTCTCAAGTTGATAGAGGACAGGGA
CTTCCCCAAGTGCACAGAGGAGATTTCAAAAGACATCAAATTCACTTTTTAAAAATGTAAAGTAGCTTTTGGTGTGCTTAAACTAGGTCAGGCCAGGCGT
GGTGGCTCATGCCTGTAATCCTAGCATTTTGGGAGGCCAAGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGATCAGCCTGGCCAACATGACGAAACCC
CTTTCTCTACTAAAAATATAAAAATTAGCTGGGCGTGGTGATGCATACCTGTAATCCCAGCTACTTCGGAGGCTGAGGCAGGAGAATCACTTGAACCTGG
GAGGCAGAGGTTGCAGTAAACTGAGACTGTGCCACTGCACTCCAGCCTGGGCAACACAGCAAGACTCTGTCTCAAAAACAAAAACAAAACTAGGCCAGGT
GCAGTGGCTCACGCTTGCAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACGAGGTCAGGATTTCGAGAACAGCCTGGCCAACATAGTGAAACCT
CGTATCTACTAAAAATACAAAAATTATCTGGGTGTGGTGGTGGGCACCTGTTGTCCCAGCTATTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGG
AGGTGGAGGTTGCAGTGAGCCAAGACCATGCCATTGCACTCCAGCCAGGTAACAGAGTGAGACTCTGTCTCAAAAAAACACACACACACACACACACAAA
ACTGTAGGTCAAAAAACATGAAAATATGTTCAACATCACTAATTAGGGAAATGTAAATCAAAAACCACAATGAACTCTTAAAATTCAACAGTAAGAAAAC
AACCTGATTAAAAACAGGCCAAAACCCTTAACATATCTCAGCAAAGAAGATAGACAGGTGGCAAATAAGCATATGAAAAGATGTTCCATATAACATGTCA
TCAGGAAAATGCAAGTTAGAACAACAGACCACTATACAACTATTAGAATGGCCAAAATCCAAAGCACCGACAGCATGAAATGCTGGGAAAGTTGGAGCAA
CCAGAACTCTTATTCCTTGCTGGTGGGAACGCAAGATGGCACAGCCACTTTGGAAGACAGTTAAGCAGTTTCTTACAAAAACTAGGTAAGCTCTTACCAT
GTGATCCAGCAATCTTGCTCTTTAGTATTTACCTGAAGGAACTGAAAACATGTCCACACAAAAACCAGCACATGGATGTTTATAGCAGCTTTATCTATAA
TTGCCAAAACTCAACCCAAAATGTCTTTCAGTAGGTAAATGGGTAAATAAATTGTGGTGCATGTAGTCATTATTCAGTGCTTAAATCAAGCTATGACAAA
TTATGAGTTATCAAGCTATAAGAAGTCACAGAGGAACTTAAATGAATGCTACTAAATGAAGCCAGTCTGAAAAGGCTTCATATTAAATGATGCCAACTAT
ATGACACTGGGATGTATTCTGGAAAAGGCAAAACTATGGAGACAGTAAAAAGCAGTGGGTGGGGGAGGGGAGGGAGGAATAATTGGAGCACAGAAGATTT
TTAGGGCAGCGAAACTACTCTGTATGATACTATAATTATAAATACCTGTCATTGTACATATGTCCAACCCCCTAAAATGTACAACACCAAGAGTGAACCC
TAATGTAAACTGTGGACTTTGAGTGATAATGATGTGTCAGTGTAGGTTCATCAATTACTGCAAATGTACCTCTTTGGTGGGAGATGTTGAAAATGGTGGA
GACTATGCATGTGTGGGGACAACAACTATATGGGAAATCTCTGTACCCTCTCAATTTTGCTGTAAACCTAAAATTGCTCTAAAATATAAAGTCTATTAAA
ACCAC

Loop counts:

4 nts: 1

Tetra-loop variants:

UUAC    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: 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