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

CAAGGCCGAGGCGCGAAGGGTGGGACCGCAGGAGCCGTGCAGCCGCGGACCAATGAGCGGGCGCCGGACGACCTGTGGCCCAATGGCGGCGGCGCGCGGG
CACGCTGGGGGCCGGCCAGACGGGCCGACTTTTCCAGAAGACCCGGATAGTTCCTCCCGGCCACGCCGCGCCGGCTCTGGGCACTCAGCATCGTTTCCTT
TTCCTCCGCTGGAGCAGCTATGGCGGCGGTGAAGACCCTGAACCCCAAGGCCGAGGTGGCCCGAGCGCAGGCGGCGCTGGCGGTCAACATCAGCGCAGCG
CGGGGTCTGCAGGACGTGCTAAGGACCAACCTGGGGCCCAAGGGCACCATGAAGATGCTCGTTTCTGGCGCTGGAGACATCAAACTTACTAAAGACGGCA
ATGTGCTGCTTCACGAAATGCAAATTCAACACCCAACAGCTTCCTTAATAGCAAAGGTAGCAACAGCCCAGGATGATATAACTGGTGATGGTACGACTTC
TAATGTCCTAATCATTGGAGAGCTGCTGAAACAGGCGGATCTCTACATTTCTGAAGGCCTTCATCCTAGAATAATCACTGAAGGATTTGAAGCTGCAAAG
GAAAAGGCCCTTCAGTTTTTGGAAGAAGTCAAAGTAAGCAGAGAGATGGACAGGGAAACACTTATAGATGTGGCCAGAACATCTCTTCGTACTAAAGTTC
ATGCTGAACTTGCAGATGTCTTAACAGAGGCTGTAGTGGACTCCATTTTGGCCATTAAAAAGCAAGATGAACCTATTGATCTCTTCATGATTGAGATCAT
GGAGATGAAACATAAATCTGAAACTGATACAAGCTTAATCAGAGGGCTTGTTTTGGACCACGGAGCACGGCATCCTGATATGAAGAAAAGGGTGGAGGAT
GCATACATCCTCACTTGTAACGTGTCATTAGAGTATGAGAAAACAGAAGTGAATTCTGGCTTTTTTTACAAGAGTGCAGAAGAGAGAGAAAAACTCGTGA
AAGCTGAAAGAAAATTCATTGAAGATAGGGTTAAAAAAATAATAGAACTGAAAAGGAAAGTCTGTGGCGATTCAGATAAAGGATTTGTTGTTATTAATCA
AAAGGGAATTGACCCCTTTTCCTTAGATGCTCTTTCAAAAGAAGGCATAGTTGCTCTGCGCAGAGCTAAAAGGAGAAATATGGAGAGGCTGACTCTTGCT
TGTGGTGGGGTAGCCCTGAATTCTTTTGACGACCTAAGTCCTGACTGCTTGGGACATGCAGGACTTGTATATGAGTATACATTGGGAGAAGAGAAGTTTA
CCTTTATTGAGAAATGTAACAACCCTCGTTCTGTCACATTATTGATCAAAGGACCAAATAAGCACACACTCACTCAGATCAAAGATGCAGTGAGGGACGG
CTTGAGGGCTGTCAAAAATGCTATTGATGATGGCTGTGTGGTTCCAGGTGCTGGTGCCGTGGAAGTGGCAATGGCAGAAGCCCTGATTAAACATAAGCCC
AGTGTAAAGGGCAGGGCACAGCTTGGAGTCCAAGCATTTGCTGATGCATTGCTCATTATTCCCAAGGTTCTTGCTCAGAACTCTGGTTTTGACCTTCAGG
AAACATTAGTTAAAATTCAAGCAGAACATTCAGAATCAGGTCAGCTTGTGGGTGTGGACCTGAACACAGGTGAGCCAATGGTGGCAGCAGAAGTAGGCGT
ATGGGATAACTATTGTGTAAAGAAACAGCTTCTTCACTCCTGCACTGTGATTGCCACCAACATTCTCTTGGTTGATGAGATCATGCGAGCTGGAATGTCT
TCTCTGAAAGGTTGAATTGAAGCTTCCTCTGTATCTGAATCTTGAAGACTGCAAAGTGATCCTGAGGATTACAGCTGTGGAATTTTTGTCCAAGCTTCAA
ATAATTTTGAAAGAAATTTTCCCATATGAAAAAAGGAGAGAACACTGGCATCTGTTGAAATTTGGAAGTTCTGAAATTATAGTATTTTTAAAAATTGCAC
TGAAGTGTATACACATAAAGCAGGTCTTTTATCCAGTGAACAGGATGTTTTGCTTTAGCAGCAGTGACATAAAATTCCATGTTAGATAAGCATATGTTAC
TTACCTTGTTATTAAATATTTCTTGAAAAGCAAATTTTAATGGTTTAATTTTATGTGGACGTATGTTAAATTATCCAACTACCCTATTGTTAAGCATTTG
GTTTTAAAATTTTTATGCTAATATAAATGCTCAAGTAATTTAAAATATTGAAAGCATCCCTGTTGGTATAAATTTCTGAGTAAATGCATTGGATCAGTTG
GACTTTGAACGCCTTTGAAATGGCTTTGCTAAAATGCTCCCGCCACAAAGTTGTAGGAAATGGGAAGAGGAGTCAACTAGAGGCAAGGGAGTTGAGAGAG
CTGCAACTGTAAAGGGCAAGAACAGGCAGAGGTAAAAAGATGATGGAAGGTGTGGTGACTAAGGGCCACGGTTATTGGGTGAAATTTGAGATTGTAGGCC
AACTGTATTTTCAAGCTTCTGAACTTAGGCAAAATATTCATCGCAAAGTCTCTAGCGTCATATTTTTCTCACCCAAATTACGTTTCCACGAGATTATTTA
TATATAGTTGGTCTATCTCTGCAGTCCTTGAAGGTGAAGTTGTGTGTTACTAGGCTGTGTTTTGGGATGTCAGCAGTGGCCTGAAGTGAGTTGTGCAATA
AATGTTAAGTTGAAACCTC

Loop counts:

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

Tetra-loop variants:

UGAG    2
UGUG    1
UAAU    1
AACU    1
CAUA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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