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

AGTCAAGTAACGCTGAGAGCCTATCGCATGAGGGCGACAGCCGGAAAGCAGGATGGAGCCATAGAAGCAATTCTCGCGAGAAGTAGAGTTGCGGTTCCCT
CGGGAGAGGGGCGGAGGCTCAGAGGTGCACCACGTGGGGTTTGCTGCCGGAGCGGAGTCTCCGGCCGGCGTCCAGTTTGAGTCTAGGTTGGAGTTGGAAC
CGTGGAGATGCGGAAGGAAACCCCACCCCCCCTAGTGCCCCCGGCGGCCCGGGAGTGGAATCTTCCCCCAAATGCGCCCGCCTGCATGGAACGGCAGTTG
GAGGCTGCGCGGTACCGGTCCGATGGGGCGCTTCTCCTCGGGGCCTCCAGCCTGAGTGGGCGCTGCTGGGCCGGCTCCCTCTGGCTTTTTAAGGACCCCT
GTGCCGCCCCCAACGAAGGCTTCTGCTCCGCCGGAGTCCAAACGGAGGCTGGAGTGGCTGACCTCACTTGGGTTGGGGAGAGAGGTATTCTAGTGGCCTC
CGATTCAGGTGCTGTTGAATTGTGGGAACTAGATGAGAATGAGACACTTATTGTCAGCAAGTTCTGCAAGTATGAGCATGATGACATTGTGTCTACAGTC
AGTGTCTTGAGCTCTGGCACACAAGCTGTCAGTGGTAGCAAAGACATCTGCATCAAGGTTTGGGACCTTGCTCAGCAGGTGGTACTGAGTTCATACCGAG
CTCATGCTGCTCAGGTCACTTGTGTTGCTGCCTCTCCTCACAAGGACTCTGTGTTTCTTTCATGCAGCGAGGACAATAGAATTTTACTCTGGGATACCCG
CTGTCCCAAGCCAGCATCACAGATTGGCTGCAGTGCGCCTGGCTACCTTCCTACCTCGCTGGCTTGGCATCCTCAGCAAAGTGAAGTCTTTGTCTTTGGT
GATGAGAATGGGACAGTCTCCCTTGTGGACACCAAGAGTACAAGCTGTGTCCTGAGCTCAGCTGTACACTCCCAGTGTGTCACTGGGCTGGTGTTCTCCC
CACACAGTGTTCCCTTCCTGGCCTCTCTCAGTGAAGACTGCTCACTTGCTGTGCTGGACTCAAGCCTTTCTGAGTTGTTTAGAAGCCAAGCCCACAGAGA
CTTTGTGAGAGATGCGACTTGGTCCCCGCTCAATCACTCCCTGCTTACCACAGTGGGCTGGGACCATCAGGTCGTCCACCACGTTGTGCCCACAGAACCT
CTCCCAGCCCCTGGACCTGCAAGTGTTACTGAGTAGATTGGATTTAAGACAAAAAGCAAGTCCCCCATGAGTGTCCACTTCTTTGCCCTGCCCTCTCAGC
TTGTGAGACAACACAGGAGCCTTCTATAGTATGTTGATATGCTAGATCTGTGCCGTTAATAGGCATCGTCTCTCAGCCTGAGGGAGGCTGGATTCTGGGT
TCCTGTAGTCACAGGGAGGAAAAGCTTTCTTAAAAATGGACATGTATGTGCGTGTGAGTGTGTGTGTAGATTTATAGTTTTTGGTAGTGGCAGGAATAAA
AAAAATCCATCCTACATCTTCCCTAAGCACTGCCTCTCTCTCACCCCCCAAAACAAGTTGACGAAAGGGTTTTATGTAGCTGTCTATGAGGAATTGGCCG
TGTCTGGGTGGGTTATGGGATGTGGGCATCCCTGGGTTCTTGGAAGCAGCTCTTATGCTACTCATAGAGATGGGATTGACTTTATTTTTTTATAGTGCTT
AATTCACCATTATGAGAAATGCTTCCAGTCACAAAAATGCAGCCCAGCTCACTCTGAGGAAGAAGCAGGACTTGGTACGGTTTTACACAACTCCTTACCA
TTAAACTGAATCAGAAATCCATTTTCTGGCTGAATAAAAAGTTTGGCTTGCCTGTGTAATGCCCACTCCCTTCCCCCTGGCTCCCTAGTGATGGGACATA
TATGAGAGAGAAGTGTTTTTCTATCATAGACACCATAGGGGAAAGTTTGGGGATGAAGGAGAGCTTAAAGGTGTTTCAATTAAGTTAGAAAACTGACACA
GGCTGTTGAGAATTCTTTGCCACTTTTCCCACCCCAAAACAGCATGGGGCCTGACATCTTCTGCCCTGGTCCCCTTTCTCTTGATGTGGAAAGTCTGAAT
GCAGTATTTATAGACTTCTAAGGTTTTAAAATCCAGTATCAAGAAGAAAATCAGAAATACTGGTTGGTGAAATAAAGAGTTTAGGCATTGTTGGCCTGTC
TTTTTTGAAGCATGTGTGTTATGTGTAGTTAGATATATTTCACTTATGTGAGTCATCATGGTGTTGGTCTTGTAGCCCATTATTTTTCCTGTGCTTCCCC
AGCTTCCCAAAGTAGCTAGTTAGAACTTAAGGTAAATATTTATTCTTGGGTTGGTGGAGTGGATATTGCCAGTTAGGAGTCATGGATCAATTACTGATTA
TATTGAAAGTAAATATAATCAATTATGTACTTTTGAGCTTTGCAGGTTCAATTTAGGTAAAAATCACATTATGAAACTGGGAAAGTCTGAAGGAATATGG
GCAAAATATTTCTCAGTAAAGCTTCCATGCTTCACCCTTGACATGATTACCCTTGAGTAAAACATGGGAATTTGTA

Loop counts:

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

Tetra-loop variants:

UUGA    1
GUGU    1
AGAA    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: 1
G x A bulge: 2
G x U bulge: 0
G x C bulge: 0
A x G bulge: 2
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: 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