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

AGCCCCGGTAGCTGAGGGACGCAGCTAGACCTTGGCGGGACGGGGCTTTCGCCGGGGCCCAGGCCCAGGGACCAGGCGGAGGCGTCGCGGGAGCCTTTGG
GGCACCACAGAGATGCGGGTTTGCCTGCAATGAGATTTCATTCTCTACATTTAAAGGACATCCTTTCTGAGCTGCTGTGAATAAATTTGGAATGGTACTG
TATATTTTCATCTAATGGAGAACTAGCTGTACTTTGAATAAGGATTGCTGCACTGGACGACTTTAGAACATCCCTCACAATGTCGTCAACCCGGAGCCAG
AACCCCCACGGCCTGAAGCAGATTGGCCTGGACCAGATCTGGGACGACCTCAGAGCCGGCATCCAGCAGGTGTACACACGGCAGAGCATGGCCAAGTCCA
GATATATGGAGCTCTACACTCATGTTTATAACTACTGTACTAGTGTTCACCAGTCAAACCAAGCACGAGGAGCTGGAGTTCCTCCTTCTAAGTCGAAAAA
GGGGCAGACACCTGGAGGAGCTCAGTTTGTTGGCCTGGAATTATATAAACGACTTAAGGAATTTTTGAAGAATTACTTGACAAATCTTCTTAAGGATGGA
GAAGATTTGATGGATGAGAGTGTACTGAAATTCTACACTCAACAATGGGAAGATTATCGATTTTCAAGCAAAGTGCTGAATGGAATTTGTGCCTACCTCA
ATAGACATTGGGTTCGCCGTGAATGTGACGAAGGACGAAAAGGAATATATGAAATCTATTCGCTTGCATTGGTGACTTGGAGAGACTGTCTGTTCAGGCC
ACTGAATAAACAGGTAACAAATGCTGTTTTAAAGCTGATTGAAAAGGAAAGGAATGGTGAAACCATCAATACAAGATTGATTAGTGGAGTTGTACAGTCT
TACGTGGAATTGGGGCTGAATGAAGATGATGCATTTGCAAAGGGCCCTACGTTAACAGTGTATAAAGAATCCTTTGAATCTCAATTTTTGGCTGACACAG
AGAGATTTTATACCAGAGAGAGTACTGAATTCTTGCAGCAGAACCCAGTTACTGAATATATGAAAAAGGCAGAGGCTCGTCTGCTTGAGGAACAACGAAG
AGTTCAGGTTTACCTTCATGAAAGCACACAAGATGAATTAGCAAGGAAATGTGAACAAGTCCTCATTGAAAAACACTTGGAAATTTTCCACACAGAATTT
CAGAATTTATTGGATGCTGACAAAAATGAAGATTTGGGACGCATGTATAATCTTGTATCTAGAATCCAGGATGGCCTAGGAGAATTGAAAAAACTGTTGG
AGACACACATTCATAATCAGGGTCTTGCAGCCATTGAAAAGTGTGGAGAAGCTGCTTTAAATGACCCCAAAATGTATGTACAGACAGTGCTTGATGTTCA
TAAAAAATACAATGCCCTGGTAATGTCTGCATTCAACAATGACGCTGGCTTTGTGGCTGCTCTTGATAAGGCTTGTGGTCGCTTCATAAACAACAACGCG
GTTACCAAGATGGCCCAATCATCCAGTAAATCCCCTGAGTTGCTGGCTCGATACTGTGACTCCTTGTTGAAGAAAAGTTCCAAGAACCCAGAGGAGGCAG
AACTAGAAGACACACTCAATCAAGTGATGGTTGTCTTCAAGTACATAGAAGACAAAGACGTATTTCAGAAGTTCTATGCGAAGATGCTCGCCAAGAGGCT
CGTCCACCAGAACAGTGCAAGTGACGATGCCGAAGCCAGCATGATCTCCAAGTTAAAGCAAGCTTGCGGGTTCGAGTACACCTCTAAACTTCAGCGCATG
TTTCAAGACATTGGCGTGAGCAAAGATCTGAACGAGCAATTCAAAAAGCACTTGACAAACTCAGAACCCCTAGACTTGGATTTCAGCATTCAAGTGCTGA
GCTCCGGGTCCTGGCCCTTCCAGCAGTCTTGTACATTTGCCTTGCCGTCAGAGTTGGAACGTAGTTATCAGCGATTCACAGCTTTCTACGCCAGCCGCCA
CAGTGGCCGAAAATTGACGTGGTTATATCAGTTGTCTAAAGGAGAATTGGTAACTAACTGCTTCAAAAACAGATATACTTTGCAGGCGTCGACATTCCAG
ATGGCTATCCTGCTTCAGTACAACACGGAAGATGCCTACACTGTGCAGCAGCTGACCGACAGCACTCAAATTAAAATGGACATTTTGGCGCAAGTTTTAC
AGATTTTATTAAAGTCGAAGCTATTGGTCTTGGAAGATGAAAATGCAAATGTTGATGAGGTGGAATTGAAGCCAGATACCTTAATAAAATTATATCTTGG
TTATAAAAATAAGAAATTAAGGGTTAACATCAATGTGCCAATGAAAACCGAACAGAAGCAGGAACAAGAAACCACACACAAAAACATCGAGGAAGACCGC
AAACTACTGATTCAGGCGGCCATCGTGAGAATCATGAAGATGAGGAAGGTTCTGAAACACCAGCAGTTACTTGGCGAGGTCCTCACTCAGCTGTCCTCCA
GGTTCAAACCTCGAGTCCCTGTGATCAAGAAATGCATTGACATTCTAATTGAGAAAGAATATTTGGAGCGAGTGGATGGTGAAAAGGACACCTACAGTTA
CTTGGCTTAACCCTTCTGGAAGGGTCTGACTGTGTGACCCGCAGCAAATAGTTCATGTTGGAAAGAATGAAAACAACTCAAGTTCATAGCAGCCAGCCTG
CCGCCATTGGACCTCCCTTTTAAAAACTGAGACCAAGACTCCCATCAGCTGGTCTCGGATTTACATCGGAACTGCTCAGGATTGATACATTTCAAGTCTG
TAAATACGGACACCAACGCCATTTACCCTAATTTAAGAACAGCGGGGACTGACCCTCCGTGCCGAGGGCTGCATGCTACCGCACTAAGTCAATACATGGG
CTCCCCGATTCGCAGCTGTCGTCTTGGCAGCACTTGTCACGTTGGCAGCACTTTGAGAGCAAGTCTGAGTGGACCCACATGTAACCTGCTATGAAAACCA
TTTGTATAGTGTGTTTCATTTTTTAATGTGTGAAAATAAAGAAAATTAAAGGATTTCTGTACAA

Loop counts:

4 nts: 1
5 nts: 1
6 nts: 2

Tetra-loop variants:

AAAU    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: 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