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

AGAGTCCTGGCGAGGGCGCTGGCCGAGAGGTGCTCGGCTTGTAGCAGGTCCCGCACTCCAGCCTCTCGCTGCCAGGGTTTGCTCTCTGCTTGTCCTGGGC
TGAGGTGTCCATGACGGAGTCATCCAAGGAGGAAAAAATCTGTTCCGGGTGAGCCCAGGCCGCCCCGGATATGCGATGGCTGAGGAGCAGACACCAGGGA
CCACACTGAGGTTGGGTTTCAGACCAAGACACTGGATTCTCCTAGTTAAGATAAAGAGCTTTGGGTGCCTGACAGTGAAAATGGTGTAATCTGCGTTAAC
AGTTCACAGCTTGAAGGCATGACAATTAAAGAACACACATGGACTTGTGGCACATGGAAATGTGCGCACAGAAAAAGGAAATCTATAATTCTTTTAAAGT
AGGAAGGCATTCTTCCTTGCCAAAATGGGTACATTCTGTTCGGTTATCAAGTTTGAAAATCTACAAGAATTAAAGAGACTGTGTCACTGGGGTCCCATCA
TAGCCCTTGGTGTTATAGCAATATGTTCTACCATGGCCATGATTGACTCTGTGTTGTGGTATTGGCCCTTACATACAACTGGAGGAAGTGTGAATTTCAT
CATGTTGATAAATTGGACTGTCATGATTCTTTATAATTACTTCAATGCCATGTTTGTCGGTCCGGGCTTTGTCCCTCTGGGGTGGAAACCGGAAATTTCT
CAGGATACCATGTATCTCCAGTATTGTAAAGTCTGCCAAGCATACAAGGCACCACGTTCACATCACTGCAGAAAGTGTAACAGATGTGTGATGAAGATGG
ACCATCACTGTCCTTGGATCAACAACTGTTGTGGTTACCAAAATCATGCTTCGTTCACACTGTTTCTCCTTTTAGCACCACTGGGTTGTATCCATGCTGC
TTTCATTTTTGTGATGACTATGTACACACAGCTTTATCATCGGCTCTCCTTTGGGTGGAACACAGTGAAGATCGACATGAGTGCAGCCCGGAGAGATCCT
CTTCCAATTGTTCCATTTGGATTAGCTGCATTTGCTACCACCTTGTTTGCCTTGGGATTAGCTTTAGGAACAACCATAGCTGTTGGGATGTTGTTTTTTA
TCCAGATGAAAATAATTCTCAGAAACAAAACTTCTATTGAGTCATGGATTGAAGAGAAGGCTAAAGATCGAATTCAGTATTATCAACTAGATGAAGTCTT
TGTTTTTCCATATGATATGGGAAGTAGATGGAGGAACTTTAAACAGGTATTTACGTGGTCAGGGGTCCCTGAAGGAGATGGACTTGAGTGGCCAGTAAGA
GAAGGCTGTCACCAATACAGCTTAACAATAGAACAGTTGAAACAAAAAGCAGATAAGAGAGTCAGAAGTGTTCGCTATAAAGTAATAGAAGATTATAGTG
GTGCCTGCTGCCCTCTGAATAAAGGAATCAAAACCTTCTTCACAAGTCCCTGCACCGAAGAGCCTCGAATACAGCTGCAAAAAGGGGAATTCATTTTAGC
CACAAGAGGTTTACGATACTGGTTATATGGAGACAAAATTCTTGATGATTCCTTTATAGAAGGTGTTTCAAGAATAAGGGGTTGGTTCCCTAGAAAATGT
GTGGAAAAGTGTCCCTGTGATGCTGAAACAGATCAAGCCCCAGAGGGGGAGAAGAAAAATAGATAGCTGCTGTTAAAACAAAATTATCCTTTAAGTCTGC
TTAATTACTTGAAAATTGTACATATTACTAAAGAATTATGCAATGAGCCTACTCTGGTTAAGATGTTCTTTTCCTCAAAGGTGCCCTAGTGCCATGATTT
AAATATTTTTATTACCATTTTGAAATGGAGAAGCCATTCTGCATATGCCTTTGAATTCCTGCCCCTCTTTACCACCTCTTCCTCCCCCTCAAAGGAAAAA
CATTTCATCCAAGTAAGTTAACGGCATTTTCTGTAGGATTTTCTTATGCACTGCACACTCTGGACCTCACCTGCAGATACAGTTCCCCCCTTGCCAGGAG
CATCTGCATGTGGTACTTCTCTTTTCCCTCAGTTGATATTTCTTATATGATATTCTAGATACTATAGAACTCAATTTGTCAGATTCAGTATAACCTCAGA
TTTTGTTACCTGTCTTTTAAAAATGCAGATTTTGTCAAATCAAATAAAGATCAATGGATGTTGGGTATAA

Loop counts:

5 nts: 1
7 nts: 1
9 nts: 1
10 nts: 3

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