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

CCCTGCGTCTCTGCCCGCCCCGTGGCGCCCGAGTGCACTGAAGATGGCGGCTGCTGTAGGACGGTTGCTCCGAGCGTCGGTTGCCCGACATGTGAGTGCC
ATTCCTTGGGGCATTTCTGCCACTGCAGCCCTCAGGCCTGCTGCATGTGGAAGAACGAGCTTGACAAATTTATTGTGTTCTGGTTCCAGTCAAGCAAAAT
TATTCAGCACCAGTTCCTCATGCCATGCACCTGCTGTCACCCAGCATGCACCCTATTTTAAGGGTACAGCCGTTGTCAATGGAGAGTTCAAAGACCTAAG
CCTTGATGACTTTAAGGGGAAATATTTGGTGCTTTTCTTCTATCCTTTGGATTTCACCTTTGTGTGTCCTACAGAAATTGTTGCTTTTAGTGACAAAGCT
AACGAATTTCACGACGTGAACTGTGAAGTTGTCGCAGTCTCAGTGGATTCCCACTTTAGCCATCTTGCCTGGATAAATACACCAAGAAAGAATGGTGGTT
TGGGCCACATGAACATCGCACTCTTGTCAGACTTAACTAAGCAGATTTCCCGAGACTACGGTGTGCTGTTAGAAGGTTCTGGTCTTGCACTAAGAGGTCT
CTTCATAATTGACCCCAATGGAGTCATCAAGCATTTGAGCGTCAACGATCTCCCAGTGGGCCGAAGCGTGGAAGAAACCCTCCGCTTGGTGAAGGCGTTC
CAGTATGTAGAAACACATGGAGAAGTCTGCCCAGCGAACTGGACACCGGATTCTCCTACGATCAAGCCAAGTCCAGCTGCTTCCAAAGAGTACTTTCAGA
AGGTAAATCAGTAGATCACCCATGTGTATCTGCACCTTCTCAACTGAGAGAAGAACCACAGTTGAAACCTGCTTTTATCATTTTCAAGATGGTTATTTGT
AGAAGGCAAGGAACCAATTATGCTTGTATTCATAAGTATTACTCTAAATGTTTTGTTTTTGTAATTCTGGCTAAGACCTTTTAAACATGGTTAGTTGCTA
GTACAAGGAATCCTTTATTGGTAACATCTTGGTGGCTGGCTAGCTAGTTTCTACAGAACATAATTTGCCTCTATAGAAGGCTATTCTTAGATCATGTCTC
AATGGAAACACTCTTCTTTCTTAGCCTTACTTGAATCTTGCCTATAATAAAGTAGAGCAACACACATTGAAAGCTTCTGATCAACGGTCCTGAAATTTTC
ATCTTGAATGTCTTTGTATTAAACTGAATTTTCTTTTAAGCTAACAAAGATCATAATTTTCAATGATTAGCCGTGTAACTCCTGCAATGAATGTTTATGT
GATTGAAGCAAATGTGAATCGTATTATTTTAAAAAGTGGCAGAGTGACTTAACTGATCATGCATGATCCCTCATCCCTGAAATTGAGTTTATGTAGTCAT
TTTACTTATTTTATTCATTAGCTAACTTTGTCTATGTATATTTCTAGATATTGATTAGTGTAATCGATTATAAAGGATATTTATCAAATCCAGGGATTGC
ATTTTGAAATTATAATTATTTTCTTTGCTGAAGTATTCATTGTAAAACATACAAAATAAACATATTTTAAAACATTTGCATTTTACCACCA

Loop counts:

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

Tetra-loop variants:

AUUU    1
AUGU    1
UGCA    1
CAAA    1
UUGC    1
CCAU    1
AUUC    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 2
U x 0 bulge: 3
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