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

TTTTCCGACAGAGGCCTGCCCGTGATTGGCTGCTCGTACTATTTACGTCCTTTCGATGTTGCGTCATGCAGTGCGCCGGAGGAACTGTGCTCTTTGAGGC
CGACGCTAGGGGCCCGGAAGGGAAACTGCGAGGCGAAGGTGACCGGGGACCGAGCATTTCAGATCTGCTCGGTAGACCTGGTGCACCACCACCATGTTGG
CTGCAAGGCTGGTGTGTCTCCGGACACTACCTTCTAGGGTTTTCCACCCAGCTTTCACCAAGGCCTCCCCTGTTGTGAAGAATTCCATCACGAAGAATCA
ATGGCTGTTAACACCTAGCAGGGAATATGCCACCAAAACAAGAATTGGGATCCGGCGTGGGAGAACTGGCCAAGAACTCAAAGAGGCAGCATTGGAACCA
TCGATGGAAAAAATATTTAAAATTGATCAGATGGGAAGATGGTTTGTTGCTGGAGGGGCTGCTGTTGGTCTTGGAGCATTGTGCTACTATGGCTTGGGAC
TGTCTAATGAGATTGGAGCTATTGAAAAGGCTGTAATTTGGCCTCAGTATGTCAAGGATAGAATTCATTCCACCTATATGTACTTAGCAGGGAGTATTGG
TTTAACAGCTTTGTCTGCCATAGCAATCAGCAGAACGCCTGTTCTCATGAACTTCATGATGAGAGGCTCTTGGGTGACAATTGGTGTGACCTTTGCAGCC
ATGGTTGGAGCTGGAATGCTGGTACGATCAATACCATATGACCAGAGCCCAGGCCCAAAGCATCTTGCTTGGTTGCTACATTCTGGTGTGATGGGTGCAG
TGGTGGCTCCTCTGACAATATTAGGGGGTCCTCTTCTCATCAGAGCTGCATGGTACACAGCTGGCATTGTGGGAGGCCTCTCCACTGTGGCCATGTGTGC
GCCCAGTGAAAAGTTTCTGAACATGGGTGCACCCCTGGGAGTGGGCCTGGGTCTCGTCTTTGTGTCCTCATTGGGATCTATGTTTCTTCCACCTACCACC
GTGGCTGGTGCCACTCTTTACTCAGTGGCAATGTACGGTGGATTAGTTCTTTTCAGCATGTTCCTTCTGTATGATACCCAGAAAGTAATCAAGCGTGCAG
AAGTATCACCAATGTATGGAGTTCAAAAATATGATCCCATTAACTCGATGCTGAGTATCTACATGGATACATTAAATATATTTATGCGAGTTGCAACTAT
GCTGGCAACTGGAGGCAACAGAAAGAAATGAAGTGACTCAGCTTCTGGCTTCTCTGCTACATCAAATATCTTGTTTAATGGGGCAGATATGCATTAAATA
GTTTGTACAAGCAGCTTTCGTTGAAGTTTAGAAGATAAGAAACATGTCATCATATTTAAATGTTCCGGTAATGTGATGCCTCAGGTCTGCCTTTTTTTCT
GGAGAATAAATGCAGTAATCCTCTCCCAAATAAGCACACACATTTTCAATTCTCATGTTTGAGTGATTTTAAAATGTTTTGGTGAATGTGAAAACTAAAG
TTTGTGTCATGAGAATGTAAGTCTTTTTTCTACTTTAAAATTTAGTAGGTTCACTGAGTAACTAAAATTTAGCAAACCTGTGTTTGCATATTTTTTTGGA
GTGCAGAATATTGTAATTAATGTCATAAGTGATTTGGAGCTTTGGTAAAGGGACCAGAGAGAAGGAGTCACCTGCAGTCTTTTGTTTTTTTAAATACTTA
GAACTTAGCACTTGTGTTATTGATTAGTGAGGAGCCAGTAAGAAACATCTGGGTATTTGGAAACAAGTGGTCATTGTTACATTCATCTGCTGAACTTAAC
AAAACTGTTCATCCTGAAACAGGCACAGGTGATGCATTCTCCTGCTGTTGCTTCTCAGTGCTCTCTTTCCAATATAGATGTGGTCATGTTTGACTTGTAC
AGAATGTTAATCATACAGAGAATCCTTGATGGAATTATATATGTGTGTTTTACTTTTGAATGTTACAAAAGGAAATAACTTTAAAACTATTCTCAAGAGA
AAATATTCAAAGCATGAAATATGTTGCTTTTTCCAGAATACAAACAGTATACTCATGATTGCTAAGTGTTTTTTTATTTTTGCATATTTATTGAACTGTC
TAATTGAATACAGCTTGCTCTTGTCACC

Loop counts:

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

Tetra-loop variants:

UGUU    2
UCCG    1
UAAG    1
UCUA    1
UUCA    1

Single bulge variants:

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