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

ACAGCACAGACAGATTGACCTATTGGGGTGTTTCGCGAGTGTGAGAGGGAAGCGCCGCGGCCTGTATTTCTAGACCTGCCCTTCGCCTGGTTCGTGGCGC
CTTGTGACCCCGGGCCCCTGCCGCCTGCAAGTCGGAAATTGCGCTGTGCTCCTGTGCTACGGCCTGTGGCTGGACTGCCTGCTGCTGCCCAACTGGCTGG
CAAGATGAAGCTCTCCCTGGTGGCCGCGATGCTGCTGCTGCTCAGCGCGGCGCGGGCCGAGGAGGAGGACAAGAAGGAGGACGTGGGCACGGTGGTCGGC
ATCGACCTGGGGACCACCTACTCCTGCGTCGGCGTGTTCAAGAACGGCCGCGTGGAGATCATCGCCAACGATCAGGGCAACCGCATCACGCCGTCCTATG
TCGCCTTCACTCCTGAAGGGGAACGTCTGATTGGCGATGCCGCCAAGAACCAGCTCACCTCCAACCCCGAGAACACGGTCTTTGACGCCAAGCGGCTCAT
CGGCCGCACGTGGAATGACCCGTCTGTGCAGCAGGACATCAAGTTCTTGCCGTTCAAGGTGGTTGAAAAGAAAACTAAACCATACATTCAAGTTGATATT
GGAGGTGGGCAAACAAAGACATTTGCTCCTGAAGAAATTTCTGCCATGGTTCTCACTAAAATGAAAGAAACCGCTGAGGCTTATTTGGGAAAGAAGGTTA
CCCATGCAGTTGTTACTGTACCAGCCTATTTTAATGATGCCCAACGCCAAGCAACCAAAGACGCTGGAACTATTGCTGGCCTAAATGTTATGAGGATCAT
CAACGAGCCTACGGCAGCTGCTATTGCTTATGGCCTGGATAAGAGGGAGGGGGAGAAGAACATCCTGGTGTTTGACCTGGGTGGCGGAACCTTCGATGTG
TCTCTTCTCACCATTGACAATGGTGTCTTCGAAGTTGTGGCCACTAATGGAGATACTCATCTGGGTGGAGAAGACTTTGACCAGCGTGTCATGGAACACT
TCATCAAACTGTACAAAAAGAAGACGGGCAAAGATGTCAGGAAAGACAATAGAGCTGTGCAGAAACTCCGGCGCGAGGTAGAAAAGGCCAAACGGGCCCT
GTCTTCTCAGCATCAAGCAAGAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGACCCTGACTCGGGCCAAATTTGAAGAGCTCAACATG
GATCTGTTCCGGTCTACTATGAAGCCCGTCCAGAAAGTGTTGGAAGATTCTGATTTGAAGAAGTCTGATATTGATGAAATTGTTCTTGTTGGTGGCTCGA
CTCGAATTCCAAAGATTCAGCAACTGGTTAAAGAGTTCTTCAATGGCAAGGAACCATCCCGTGGCATAAACCCAGATGAAGCTGTAGCGTATGGTGCTGC
TGTCCAGGCTGGTGTGCTCTCTGGTGATCAAGATACAGGTGACCTGGTACTGCTTGATGTATGTCCCCTTACACTTGGTATTGAAACTGTGGGAGGTGTC
ATGACCAAACTGATTCCAAGGAACACAGTGGTGCCTACCAAGAAGTCTCAGATCTTTTCTACAGCTTCTGATAATCAACCAACTGTTACAATCAAGGTCT
ATGAAGGTGAAAGACCCCTGACAAAAGACAATCATCTTCTGGGTACATTTGATCTGACTGGAATTCCTCCTGCTCCTCGTGGGGTCCCACAGATTGAAGT
CACCTTTGAGATAGATGTGAATGGTATTCTTCGAGTGACAGCTGAAGACAAGGGTACAGGGAACAAAAATAAGATCACAATCACCAATGACCAGAATCGC
CTGACACCTGAAGAAATCGAAAGGATGGTTAATGATGCTGAGAAGTTTGCTGAGGAAGACAAAAAGCTCAAGGAGCGCATTGATACTAGAAATGAGTTGG
AAAGCTATGCCTATTCTCTAAAGAATCAGATTGGAGATAAAGAAAAGCTGGGAGGTAAACTTTCCTCTGAAGATAAGGAGACCATGGAAAAAGCTGTAGA
AGAAAAGATTGAATGGCTGGAAAGCCACCAAGATGCTGACATTGAAGACTTCAAAGCTAAGAAGAAGGAACTGGAAGAAATTGTTCAACCAATTATCAGC
AAACTCTATGGAAGTGCAGGCCCTCCCCCAACTGGTGAAGAGGATACAGCAGAAAAAGATGAGTTGTAGACACTGATCTGCTAGTGCTGTAATATTGTAA
ATACTGGACTCAGGAACTTTTGTTAGGAAAAAATTGAAAGAACTTAAGTCTCGAATGTAATTGGAATCTTCACCTCAGAGTGGAGTTGAAACTGCTATAG
CCTAAGCGGCTGTTTACTGCTTTTCATTAGCAGTTGCTCACATGTCTTTGGGTGGGGGGGAGAAGAAGAATTGGCCATCTTAAAAAGCGGGTAAAAAACC
TGGGTTAGGGTGTGTGTTCACCTTCAAAATGTTCTATTTAACAACTGGGTCATGTGCATCTGGTGTAGGAAGTTTTTTCTACCATAAGTGACACCAATAA
ATGTTTGTTATTTACACTGGTCTAATGTTTGTGAGAAGCTTCTAATTAGATCAATTACTTATTTTAGGAAATTTAAGACTAGATACTCGTGTGTGGGGTG
AGGGGAGGGAGTATTTGGTATGTTGGGATAAGGAAACACTTCTATTTAATGCTTCCAGGGATTTTTTTTTTTTTTTTTAACCCTCCTGGGCCCAAGTGAT
CCTTCCACCTCAGTCTCCCAGCTAATTGAGACCACAGGCTTGTTACCACCATGCTCGGCTTTTGCATTAATCTAAGAAAAGGGGAGAGAAGTTAATCCAC
ATCTTTACTCAGGCAAGGGGCATTTCACAGTGCCCAAGAGTGGGGTTTTCTTGAACATACTTGGTTTCCTATTTCCCCTTATCTTTCTAAAACTGCCTTT
CTGGTGGCTTTTTTTAAAATTATTACTAATGATGCTTTTATAGCTGCTTGGATTCTCTGAGAAATGATGGGGAGTGAGTGATCACTGGTATTAACTTTAT
ACACTTGGATTTCATTTGTAACTTTAGGATGTAAAGGTATATTGTGAACCCTAGCTGTGTCAGAATCTCCATCCCTGAAATTTCTCATTAGTGGTACTGG
GGTGGGATCTTGGATGGTGACATTGAAACTACACTAAATCCCCTCACTATGAATGGGTTGTTAAAGGCAATGGTTTGTGTCAAAACTGGTTTAGGATTAC
TTAGATTGTGTTCCTGAAGAAAAGAGTCCAGGTAAATGGTATGATCAATAAAGGACAGGCTGGTGCTAACATAAAATCCAATATTGTAATCCTAGCACTT
TGGGAGGCCAAGGCGGGTGGATCACAAGGTCAAGAGATAGAGACCATCTTTGCCAACATGGTGAAACTCCATCTCTACTGAAAATACAAAAATTAGCTGG
GCGTGGTAGTGCAAGCTGAAGGCTGAGGCAGGAGAATCACTCGAACCCGGGAGGCAGAGGTTGCAGTGAGCCGAGATCACACCACTGTACTCCAGCCCGG
CACTCCAGCCTGGCGACAAGAGTGAGACTCCACCTCAAAAAAAAAAAAAAGAATCCAATACTGCCCAAGGATAGGTATTTTATAGATGGGCAACTGGCTG
AAAGGTTAATTCTCTAGGGCTAGTAGAACTGGATCCCAACACCAAACTCTTAATTAGACCTAGGCCTCAGCTGCACTGCCCGAAAAGCATTTGGGCAGAC
CCTGAGCAGAATACTGGTCTCAGGCCAAGCCCAATACAGCCATTAAAGATGACCTACAGTGCTGTGTACCCTGGGGCAATAGGGTTAAATGGTAGTTAGC
AACTAGGGCTAGTCTTCCCTTACCTCAAAGGCTCTCACTACCGTGGACCACCTAGTCTGTAACTCTTTCTGAGGAGCTGTTACTGAATATTAAAAAGATA
GACTTCAA

Loop counts:

3 nts: 5
4 nts: 7
5 nts: 5
6 nts: 2
7 nts: 3
8 nts: 3

Tetra-loop variants:

GGAA    1
GCUC    1
AAAU    1
CUCC    1
AUGC    1
CAUC    1
UGUU    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 1
U x 0 bulge: 4
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: 0
U x G bulge: 0
U x A bulge: 0
U x U bulge: 1
U x C bulge: 1
C x G bulge: 0
C x A bulge: 0
C x U bulge: 1
C x C bulge: 0