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

TGACGCGACCCAGGGTCAGGATAACATGCAGGGCGGGGATGGGCTGGGAGGGTCAGTCTCCGGGGAGGGGCGCCCTGGGCCGGGGTAAGGGAGCTCCCAG
GCCCGGGATCTCGGCTCACCGGACCGGTACCGCGCAGCCTCCAACTGCCGTTCCATGCAGGCGGGCGCATTTGGGGGAAGATTCCACTCCCGGGCCGCCG
GGGGCACTAGGGGGGGTGGGGTTTCCTTCCGCATCTCCACGGTTCCAACTCCAACCTAGACTCAAACTGGACGCCGGCCGGAGACTCCGCTCCGGCAGCA
AACCCCACGTGGTGCACCTCTGAGCCTCCGCCCCTCTCCCGAGGGAACCGCAACTCTACTTCTCGCGAGAATTGCTTCTATGGCTCCATCCTGCTTTCCG
GCTGTCGCCCTCATGCGATAGGCTCTCAGCGTTACTTGACTCTTCTCGCGATAATTTTTTTTAAAAATCTCCCAAGGAAAGTTGAAGGAAGAGTACAAAA
TTTTCATCTCGCGAGACTTGTGAGCGGCCATCTTGGTCCTGCCCTGACAGATTCTCCTATCGGGGTCACAGGGACGCTAAGATTGCTACCTGGACTTTCG
TTGACCATGCTGTCCCGGGTGGTACTTTCCGCCGCCGCCACAGCGGCCCCCTCTCTGAAGAATGCAGCCTTCCTAGGTCCAGGGGTATTGCAGGCAACAA
GGACCTTTCATACAGGGCAGCCACACCTTGTCCCTGTACCACCTCTTCCTGAATACGGAGGAAAAGTTCGTTATGGACTGATCCCTGAGGAATTCTTCCA
GTTTCTTTATCCTAAAACTGGTGTAACAGGACCCTATGTACTCGGAACTGGGCTTATCTTGTACGCTTTATCCAAAGAAATATATGTGATTAGCGCAGAG
ACCTTCACTGCCCTATCAGTACTAGGTGTAATGGTCTATGGAATTAAAAAATATGGTCCCTTTGTTGCAGACTTTGCTGATAAACTCAATGAGCAAAAAC
TTGCCCAACTAGAAGAGGCGAAGCAGGCTTCCATCCAACACATCCAGAATGCAATTGATACGGAGAAGTCACAACAGGCACTGGTTCAGAAGCGCCATTA
CCTTTTTGATGTGCAAAGGAATAACATTGCTATGGCTTTGGAAGTTACTTACCGGGAACGACTGTATAGAGTATATAAGGAAGTAAAGAATCGCCTGGAC
TATCATATATCTGTGCAGAACATGATGCGTCGAAAGGAACAAGAACACATGATAAATTGGGTGGAGAAGCACGTGGTGCAAAGCATCTCCACACAGCAGG
AAAAGGAGACAATTGCCAAGTGCATTGCGGACCTAAAGCTGCTGGCAAAGAAGGCTCAAGCACAGCCAGTTATGTAAATGTATCTATCCCAATTGAGACA
GCTAGAAACAGTTGACTGACTAAATGGAAACTAGTCTATTTGACAAAGTCTTTCTGTGTTGGTGTCTACTGAAGTTATAGTTTACCCTTCCTAAAAATGA
AAAGTTTGTTTCATATAGTGAGAGAACGAAATCTCTATCGGCCAGTCAGATGTTTCTCATCCTTCTTGCTCTGCCTTTGAGTTGTTCCGTGATCACTTCT
GAATAAGCAGTTTGCCTTTATAAAAACTTGCTGCCTGACTAAAGATTAACAGGTTATAGTTTAAATTTGTAATTAATTCTACCATCTTGCAATAAAGTGA
CAATTGAATGAAACAGGGTTTTTCAAGTTGTATAATTCTCTGAAATACTCAGCTTTTGTCATATGGGTAAAAATTAAAGATGTCATTGAACTACTGTCTT
GTTTATGAGACCATTCAGTGGTGAACTGTTTCTGGCTGATAGGTTATGAGATATGTAAAGCTTTCTAGTACTCTTAAAATAACTAAATGGAGTATTATAT
ATCAATTCATATCATTGACTTTATTATTTTAGTAGTATGCCTATAGAAAATATTATGGACTCAGAGTGTCATAAAATCACTCTTAAGAATCCATGCAGCA
GGCCAGGCACAGTGGCTCACACCTGTAATGCCTGCACTTTGGAAGGCCGAGACAGGCGGATCACTTGAGGTCAGGAGTTTGAAACCAGCCAGGCCAACAC
AGTGAAACCCTGTCTCTACTAAAAATACAAAAGGTTAGCCGGGCATGGTGGCAGGCGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGC
TTGAACGCAGGAGGCAAAGGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGACCTCGACTCCATCTAGAAAAAAAAAAAAAAAA
ATCCAGCAGACACCTATCAGGAACATAGAAAATAACAAGTGTTGGCAAGGAAGTGGAGAAGTTGGAACACTTGTGCACTGTTCGTAGAAATATGAAATGG
TACAGCCATTATGGAAAAGTGTGGTGATTCCTCATAAAATTAAAATGGAAATACCATGATCCAGCAATCCCAGTCGACATATATACTCAAAAAAATTAAA
AGCAGGGTCTTGAAGAGATACTTGTGTTCCATGGTGATAGCAGCCATTGTTCACAATAGCTAAAACATAGAAGCAGCCCAATCGGCCATCAGTAGATGAA
TGGATAAGCAAAATGTAGTATATCCATGCAATGGAATATTATTCCACTTCAAGGAAGAAAATTCTGACACTGGCTACAGCATGAATGAACCTTGAGGACG
TTATGCAGTTTTACAGGATGAGTTATGGAGCTGGATAGTGGTGATGGTGGCACATTAAGGATGTATTTAATACTGTTCTTAAATGGTACACTTAAAAATG
GTAAATTTTATGTGTATTTTACAATCTTTTTTTAAATTGAAGAAAAATCCTGTAGATAAATTAGAAAATTCTTCCCTTCATAGGTTTATCTGCATTTGAT
TCTCCCATACTTGTACAAGGATTTATTTGTATTCAAATGGACAAATTACGCAATAGGAAATATTTGAAAATATTTATCATGGGTAATTGCTATTTTCATT
GACTTCCTAAGATTTTATGTAATAATCATTTGAGTCAATATTGGTAGCTAATGTACTAATCTAATATTGAAATCAGATTGATATCTTTGTTACTTAAAGA
TAATTTGATTGGATCAGCAGTTATTTCAAATTGATTAAACAAAAAATTATAAAACA

Loop counts:

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

Tetra-loop variants:

CACA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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