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

GCGATTACTATGTGCTGGACTTCGTCGTAGTTGAGATATATTACCATCCTAAGTTAAACTATAATCGTTTATTGTTATCTCTAGGTCTTCCTAGATGAAA
TTTTTACCCTAAAGGATCGTAAAGTCGGCCCACCGGACGTCAGTGGGGTCCCCTGTTCAGCCCTCTCGTTCTTCTGGGGATCTCTCGGGACACTGACGAG
GTGGCACCGGGACCTACAGGTGGGCCGCAAGCCCCGCCCCCAGCGACGGCTTGTAGCCCCGTCCCCCGACGCAGCGCCTCTCCAAGTTTGCCCCGCCCTG
CAGGACTGCAGAATTTCCTTTCCGGCGGCGCGCTGTCGTCACGCGTCCCGCGCCTCCTCGCGCCTGCGCCGTGGTTGGAAGGTCGTCCCTGTGACCGGCT
TGGCGGTTGGAGCGGCTGTCGCCATGTTGTCGGTAGCATCCCGCTCAGGCCCGTTCGCGCCCGTCCTGTCGGCCACGTCCCGCGGGGTGGCGGGCGCGCT
GCGGCCCTTGGTGCAGGCCACGGTGCCCGCCACCCCGGAGCAGCCTGTGTTGGACCTGAAGCGGCCCTTCCTCAGCCGGGAGTCGCTGAGCGGCCAGGCC
GTGCGCCGGCCTTTGGTCGCCTCCGTGGGCCTCAATGTCCCTGCTTCTGTTTGTTATTCCCACACAGACATCAAGGTGCCTGACTTCTCTGAATACCGCC
GCCTTGAAGTTTTAGATAGTACGAAGTCTTCAAGAGAAAGCAGCGAGGCTAGGAAAGGTTTCTCCTATTTGGTAACTGGAGTAACTACTGTGGGTGTCGC
ATATGCTGCCAAGAATGCCGTCACCCAGTTCGTTTCCAGCATGAGTGCTTCTGCTGATGTGTTGGCCCTGGCGAAAATCGAAATCAAGTTATCCGATATT
CCAGAAGGCAAGAACATGGCTTTCAAATGGAGAGGCAAACCCCTGTTTGTGCGTCATAGAACCCAGAAGGAAATTGAGCAGGAAGCTGCAGTTGAATTAT
CACAGTTGAGGGACCCACAGCATGATCTAGATCGAGTAAAGAAACCTGAATGGGTTATCCTGATAGGTGTTTGCACTCATCTTGGCTGTGTACCCATTGC
AAATGCAGGAGATTTTGGTGGTTATTACTGCCCTTGCCATGGGTCACACTATGATGCATCTGGCAGGATCAGATTGGGTCCTGCTCCTCTCAACCTTGAA
GTCCCCACGTATGAGTTCACCAGTGACGATATGGTGATTGTTGGTTAAGAGACTTGGACTCAAGTCATAGGCTTCTTTCAGTCTTTATGTCACCTCAGGA
GACTTATTTGAGAGGAAGCCTTCTGTACTTGAAGTTGATTTGAAATATGTAAGAATTGATGATGTATTTGCAAACATTAATGTGAAATAAATTGAATTTA
ATGTTGAATACTTTCAGGCATTCACTTAATAAAGACACTGTTAAGCACTGTTATGCTCAGTCATACACGCGAAAGGTACAATGTCTTTTAGCTAATTCTA
ATTAAAAATTACAGACTGGTGTACAAGATACTTGTGAAATCTGTAACTGACTTTATTTTCTTGCCCAAATATTTGCTTCCTGCTTTGCGTCAGGGACGCA
GATTCTGCACGGTCATTGTTGGGATGAAGTAAAATTAACGGGTCATCTAAGTGTCTATGGCATTGACAGAAACAGTAGTATCTAGGTATTCCTTATTTAC
CGGACTTGGTAAGAGTCCTGGCTATGCATTTCCTCCCTACTGTGTAAGCCGTGTGATAATCTCAACACTAATCTGTGGGAAAGAGTCCTGAATGAGGCAT
TAGTAGCTCTGAGGGTTTATCTTCACGTCTGGTCTGCTGGTTTTTCTCCTTAAGTGACAGGCCAGGAAATTTTATTAGTCCCTTATGAGTGTAAATTAGT
ACTTAATCCTTTAGTCTTAATAGGCAGTGATGGGATATTACCTGAGAGAAACTTTCCAAAATGAGAGTGCTCTGCCATTTCGTTCATTTTGTGTGTGGTT
CATCATGTCCCCAAAGTTCCTGCATCCACTCTATCAGGAGGCAGAAAGGGAGCATCTGAGACCTAATACTGCCTGCATGCAGAAGTGGTCCTGCTGGGTT
TGTTTCTGTAGTGATGACACTTTGAATGTTTTTTCCTGTTGGGTTTACAGTCACTCAGCACTTTTCACTGTAAGATGGTGTGGAACCAGACGCAGAGCAC
ATCGGAATTCACATCCTATTCTGCCTCCAATTACACAGGTGAAACAAGACTAAGGTCCATTTTCCCCTGGGAGTTGGGAGTGGGCTTTGTCCTTTGAGAA
TCACAGTCACTTTTTGATGTGTTTGTCTTTGCTGTTTAGAGGTGGACCAGTCGTGCTTTACTGAGTCTACCTGATAATCTCATGTACACTTTTTTAAAAT
GGCAAAAATGGTTAGGTTGGGTCTGCCCAAAGGGAACTGACCATCCAGGATTCCAGCCTTTGATGTTAATAGCTAGGTGTTGACAGAAAAAAGAAAATGT
CAAACTTTCTATGCTTATGAGTAGATACTAGTCTTTGCTTCATTTTTACCATTCTAGAAATGAAATTAGCATGTGTGATAATTGGTGGGACACAGAAGTA
TTTTATATTCTGTGTCTCTAGATAGTGGAGGCACTCTTCGGATTGGGGGTTGGAGGAAGGGTTGGTGGCAGAGTTGGAATGTGAAACATTGAGTTGTGAG
GGGAACACAGGTCCACACACTAAAAAACCTGTGCTGCCAAAAATGTCAACAGCACCCCCTCCCTATAGAGAAATACTGATAACCTATATCACCTCCCACC
CTGAAGTGATACCTTGAAATTCTACATGGCAGTGGAGGACAGAAGTAGGAAGTTTGCAGGTCTCTAGGTACTCACTTAGTGCCGGAATTGCTATATTTGG
TGGCTGCTTACTTCATCTTTCATATTTAGAGTTTGATGGTGGGATGCTGTTAAATTGTAGTAGACCATTTAGTTTTTAAAGAAGGCTTTGTTCCACAAGT
GACAGGACAAGTCAAGTCACTTCATGCTGTTTTGCTGAATGGATACGGCAGACCTGTGTTAACATTTTTACCATTCTGTGAAAACAAAATCCTAGATAGT
AGGAGAAAATTACTTACAGAATAAACCTGACCAGCTAGCACCCTGACATCAGATCATTAACCTACTGCATTTTATTGGGGATAATTCTTGGGACAATCTT
GAGAGCCAAGTGTTTTCATTATGCTTTAAAAAGTGTTATAAAAATGGCCTTTTTGAAAATGTTGCATTATTTGTTAAAGATAACATCAAATTTTCTTTGG
TCTTTCTGAGCATACCTTTGTAAAAACTTTGACTCAATCTGAGTGTATAGAGGGCATTTGTCCTGACTGGATCAAAATGTGCTTTAGTACCCTCATTTTT
CTAAACTGTAGGAACATACTATTTAAATATCAGAAGTAATTCTTCATTCTCACAGTACTAAATTTCATTTTCTGT

Loop counts:

3 nts: 1
4 nts: 2
6 nts: 2

Tetra-loop variants:

CCCU    1
AAAU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 1
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