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

ACATTACAATGCCTGACAAATCCTAGCCAGTTCTATCAAATTATATCTTTCTTACAGGCTTTTAAGCTATTAGTCTCATAAAGATACATTTAATCAGCGA
GGTAATGGCATGATGAGTGTTTTTAGGTTAAAAAGAGAACAGGAACTGTTGCCAGCAGAATGGCGATATTCAAGACAACACGCACAAGAAGAGGCGGGTC
CTACGCGCTTCGCTAGGGAAGCCCGGGTCAGCTCGCTGCGCAGGCGCAGTGAGTTCGACACACCATGCCGACTGTCAGCGTGAAGCGTGATCTGCTCTTC
CAAGCCCTGGGCCGCACCTACACTGACGAAGAATTTGATGAACTATGTTTTGAATTTGGTCTGGAGCTTGATGAAATTACATCTGAGAAGGAAATAATAA
GTAAAGAACAAGGTAATGTAAAGGCAGCAGGAGCCTCTGATGTTGTTCTTTACAAAATTGACGTCCCTGCCAATAGATATGATCTCCTGTGTCTGGAAGG
ATTGGTTCGAGGACTTCAGGTCTTCAAAGAAAGGATAAAGGCTCCAGTGTATAAACGGGTAATGCCTGATGGAAAAATCCAGAAATTGATTATCACAGAA
GAGACAGCTAAGATACGTCCTTTTGCGGTAGCAGCAGTTCTCCGTAATATAAAGTTTACTAAAGATCGATATGACAGCTTCATTGAACTTCAGGAGAAAT
TACATCAGAATATTTGCAGGAAAAGAGCACTGGTTGCCATTGGTACCCATGATTTGGACACTTTGTCGGGCCCATTTACTTATACTGCAAAGCGTCCTTC
AGATATCAAATTCAAGCCTCTAAATAAGACCAAGGAGTATACAGCCTGTGAACTGATGAACATATACAAGACTGACAATCACCTGAAACATTATTTACAT
ATCATTGAAAACAAACCCCTGTATCCAGTTATCTATGATAGCAATGGTGTCGTCCTTTCAATGCCTCCCATCATCAATGGGGATCATTCCAGAATAACAG
TAAATACTAGAAATATTTTTATTGAATGCACGGGAACTGACTTTACTAAGGCAAAAATAGTTCTTGATATTATTGTCACCATGTTCAGTGAATATTGTGA
GAATCAATTTACGGTCGAAGCTGCTGAAGTGGTTTTTCCTAATGGAAAATCACATACCTTTCCAGAATTAGCTTACCGAAAGGAGATGGTGAGAGCTGAC
CTAATTAACAAAAAAGTTGGAATCAGAGAAACTCCAGAAAATCTTGCCAAACTTCTGACCAGGATGTATTTAAAATCAGAAGTCATAGGTGATGGGAATC
AGATTGAGATTGAAATCCCTCCAACCAGAGCTGACATTATCCATGCATGTGATATTGTAGAAGATGCAGCTATTGCTTATGGATATAACAACATTCAGAT
GACTCTCCCGAAAACTTACACCATAGCTAATCAATTTCCTCTTAATAAGCTCACTGAACTTCTCCGACATGACATGGCAGCCGCTGGCTTCACTGAAGCA
CTTACCTTTGCCCTGTGCTCCCAAGAAGATATTGCTGATAAACTAGGTGTGGATATCTCTGCAACAAAGGCAGTCCACATAAGTAATCCTAAAACAGCTG
AATTTCAGGTGGCACGCACTACCCTTCTTCCTGGCCTCCTGAAGACCATAGCAGCAAATCGTAAGATGCCCCTTCCACTGAAACTGTTTGAAATCTCTGA
CATTGTAATAAAAGATTCTAATACAGATGTAGGTGCAAAAAACTACAGACATCTCTGTGCTGTTTATTACAACAAGAATCCTGGGTTTGAGATCATTCAT
GGGCTGCTGGACAGAATTATGCAGTTGCTCGATGTGCCTCCTGGTGAAGACAAGGGGGGATATGTGATCAAAGCATCAGAAGGGCCTGCTTTCTTCCCCG
GGCGATGTGCAGAGATCTTTGCCAGGGGTCAAAGCGTCGGGAAGCTTGGGGTCCTTCATCCTGACGTTATCACCAAATTTGAGCTGACCATGCCCTGCTC
CTCCCTAGAAATCAATGTTGGACCCTTTTTGTGAAGATTGGTCTCTGTGGTGTGATTCTCTTCCCAGGTGTCCCTTTCTCCTCCCCTAGTGTCCTTAAGT
CCTCCTCCACAGGGAACATCTATTTGGGCTTTGATGTTTAATAAAGTAGAAAGCACTGTCTGGCTGTGTGGGTAGAGACCATCCTTTCCCTGCATATTAG
GCCAGCTTGTGCCATATACCAGTGTGGTGTCTGTGTGTGAAGCTGCATTGTTGGGTAAAAGCCCCGTGGAGTGCTGGAGAAATGCACTAGCAGAGTGCAG
GATCTGTTCTGAAAGGCAGACGTGCTCCTCAGACATCAGAACATCACATTGGAACGGATTACTCCTGCATAACAAGATCCCATTTCTTTCCTTATTGATA
AAACAAGATAATCGATGAGAATTCATGTTGCATGAGTTCGAGATAACTGAGGGGTTTAGCTTTGATTTTCTACATTTGACATGTATTCATCATTGAGAAA
CACTAAAATAACAATATTTTTAGAAAACGTTTAAGAATCAATTATGGTCCAACAATTATAGCTTCTGAGGTCAGTTTAAAGTGAAAGAAAAATCTGTAAT
ACAAGGATTCAAAATATGTGAGGGTGCATAGGTATTTTTTACTCTATCTGTGATACTCTAAGATAGAGTACATGCAACAAAGATCTGTTCTGCTGTAAGA
GTTAAAATGGACAAGTATTGATATCAATGCAGTATGAACATTAGGAAACAATGAGAAGCTTATTTTTGCCATAGGCCATACATGTTACTGTAATCAGTCA
GTTATAAAATCATGGTTTTAAATACTTAATTGAGCTACTAGTTTCTCTATTGTCCCAGGGAGATATTAGACCTCTCTTTTTCTGAAGCTAAGCTTCAGCC
AATCCTCCTTGTTTTATATCCTAATTTCCTTTCTTACTTCAATCTAGAATTCTCCAGTAGGTACCATCTCTGGAAAAAAGCTGGGTCTCATGTTTGAGAC
AAGTTCCCAGGTACTATTGAAGTAATAAGAAATATGATAAAATATAATACTTTAAAGTCCCAGTAGAAATAGCTAACAAAGGCTGGGTGCGCTGTGGCTC
ATGCCTGTAATCCTAGCACTTTGGGAGGCTGAGGTGGGCAGATCACTTGAGGCCAATAGTTCGAGATCAGCCTGACCAACATGGTGAAATGCCATCTCCA
CTAAAAATATAAAAATTAGCCAGGCATGGTGGTGTGGGCCTGCAGTCCCAGCTACCTGGGAGGCTGAGTCAGGAAAATCTCTTGAACCAGGAGGTGGACG
TTGCAGTGATCCCAGATTGTGCCACTGCCCTCCAGCCTGGGTGACAGAGTGAGATTCTGTCTACAAAAA

Loop counts:

3 nts: 3
4 nts: 4
5 nts: 1
6 nts: 1
7 nts: 2
8 nts: 1

Tetra-loop variants:

GAAG    1
GUCC    1
UUGU    1
AAAA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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