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

GCTGGCACCTTCCTGAGATATGCCTGCTTGCCCCCGATTTTTTTCTCCTTGCAGTGAGAACCTCCTCATGTGGCATCTTTACTTATTCTCTTCTTGGAAA
ATCCATGTGACCTCCCCGCGCTTAAAGTGTTTCCACGTTACAGGCGACTTAAAGGCAGCCCTGGAGCCTGACGTATAATTCGAGCGCCGATGCAGAAAGG
AGTCAGGTGTTTTTTTTTTTTTTTTTTTGGTTTCCGGTTCTGTCACCTCCAGGCTGAGCCGGGCTGGCGGAAGAGGCACGTGCGCTGCTGAATGGAGCTG
GTCGCTGGTTGCTACGAGCAGGTCCTCTTTGGGTTCGCTGTACACCCGGAGCCCGAGGCTTGCGGCGACCACGAGCAATGGACTCTTGTGGCTGACTTCA
CTCACCATGCTCACACTGCCTCCTTGTCAGCAGTAGCTGTAAATAGTCGTTTTGTGGTCACTGGGAGCAAAGATGAAACAATTCACATTTATGACATGAA
AAAGAAGATTGAGCATGGGGCTCTAGTGCATCACAGTGGTACAATAACTTGCCTGAAATTCTATGGCAACAGGCATTTAATCAGTGGAGCGGAAGATGGA
CTCATCTGTATCTGGGATGCAAAGAAATGGGAATGCCTGAAGTCAATTAAAGCTCACAAAGGACAGGTGACCTTCCTTTCTATTCACCCATCTGGCAAGT
TGGCCCTGTCGGTTGGTACAGATAAAACTTTAAGAACGTGGAATCTTGTAGAAGGAAGATCAGCATTCATAAAAAATATAAAACAAAATGCTCACATAGT
AGAATGGTCCCCAAGAGGAGAGCAGTATGTAGTTATCATACAGAATAAAATAGACATCTATCAGCTTGACACTGCATCCATTAGTGGCACCATCACAAAT
GAAAAGAGAATTTCCTCTGTTAAATTTCTTTCAGAGTCTGTCCTTGCAGTGGCTGGAGATGAAGAAGTTATAAGGTTTTTTGACTGTGATTCACTAGTGT
GCCTCTGCGAATTTAAAGCTCATGAAAACAGGGTAAAGGACATGTTCAGTTTTGAAATTCCAGAGCATCATGTTATTGTTTCAGCATCGAGTGATGGTTT
CATCAAAATGTGGAAGCTTAAGCAGGATAAGAAAGTTCCCCCATCTTTACTCTGTGAAATAAACACTAATGCCAGGCTGACGTGTCTTGGAGTGTGGCTA
GACAAAGTGGCAGACATGAAAGAAAGCCTTCCTCCAGCTGCAGAGCCTTCTCCTGTAAGTAAAGAACAGTCCAAAATTGGCAAAAAGGAGCCTGGTGACA
CAGTGCACAAAGAAGAAAAGCGGTCAAAACCTAACACAAAGAAACGCGGTTTAACAGGTGACAGTAAGAAAGCAACAAAAGAAAGTGGCCTGATATCAAC
CAAGAAGAGGAAAATGGTAGAAATGTTGGAAAAGAAGAGGAAAAAGAAGAAAATAAAAACAATGCAGTGAATCACAGATGTCTCCTGAAAGAACTCTTTT
AGATGAAATCATTCTACTCAAATGTACCTTAATTTTTTTTTTTTCCCTGAGTAAAAGCAAGAAATTTCTTCCTTTGGAAAAAATATATATATTAAAAAAC
CACTTTTAGATGGTTTTTTTTAAAAAAAAAAAAAAAACTGGTAAAATTACTTTTGGCAGACAGTGTTTTATGAATTATGTATCATGTTGATATATAATAT
GTTAATGTGTCATGTAATTTTTACTTTGTACAAAGCAAATAAAGATCTTTCTCAAAATATACTGTAAAATAATATAAAATATTGAACACATTCTTTATCA

Loop counts:

4 nts: 4
5 nts: 3
7 nts: 1
8 nts: 1

Tetra-loop variants:

AACU    1
UUAC    1
ACAA    1
GACU    1

Single bulge variants:

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

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: 2
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