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

CGCCGTAGGAGGAGGTGGAGGAGGAGGCGGCTCGGGAGAGCGAGCAGCGAGCTGGCTGGATCGCCGAGCGCGAGTGAGGGAGCCGAGCCGCCCGCCGCCG
CCGCCTCCGCCTCCCCTCCGCGAACAGGAGCCCGGGCCGGGGCCCGGCACGCCGCCCCAGCCCGTCCCTCGGCGTCAGGCCGCGAGGGTAGCGCGCGCGA
GCGAGCGAGGGGGAGGGAGAGCGAGCGAGCGCCGGGAGGAGGCGGCCGGACCGAGCGGGCGCCCGCGCGTGTGGCGTGAGGGGAAGCCGCTTGCCCGCCC
CCTTCGCCTTCCCTTCTCTCCCCCTCCCCGCTCCCCCCCCGACCGCGGAGCAGCACCATGTCGGCGCCGGCGGCCAAAGTCAGTAAAAAGGAGCTCAACT
CCAACCACGACGGGGCCGACGAGACCTCAGAAAAAGAACAGCAAGAAGCGATTGAACACATTGATGAAGTACAAAATGAAATAGACAGACTTAATGAACA
AGCCAGTGAGGAGATTTTGAAAGTAGAACAGAAATATAACAAACTCCGCCAACCATTTTTTCAGAAGAGGTCAGAATTGATCGCCAAAATCCCAAATTTT
TGGGTAACAACATTTGTCAACCATCCACAAGTGTCTGCACTGCTTGGGGAGGAAGATGAAGAGGCACTGCATTATTTGACCAGAGTTGAAGTGACAGAAT
TTGAAGATATTAAATCAGGTTACAGAATAGATTTTTATTTTGATGAAAATCCTTACTTTGAAAATAAAGTTCTCTCCAAAGAATTTCATCTGAATGAGAG
TGGTGATCCATCTTCGAAGTCCACCGAAATCAAATGGAAATCTGGAAAGGATTTGACGAAACGTTCGAGTCAAACGCAGAATAAAGCCAGCAGGAAGAGG
CAGCATGAGGAACCAGAGAGCTTCTTTACCTGGTTTACTGACCATTCTGATGCAGGTGCTGATGAGTTAGGAGAGGTCATCAAAGATGATATTTGGCCAA
ACCCATTACAGTACTACTTGGTTCCCGATATGGATGATGAAGAAGGAGAAGGAGAAGAAGATGATGATGATGATGAAGAGGAGGAAGGATTAGAAGATAT
TGACGAAGAAGGGGATGAGGATGAAGGTGAAGAAGATGAAGATGATGATGAAGGGGAGGAAGGAGAGGAGGATGAAGGAGAAGATGACTAAATAGAACAC
TGATGGATTCCAACCTTCCTTTTTTTAAATTTTCTCCAGTCCCTGGGAGCAAGTTGCAGTCTTTTTTTTTTTTTTTTTTTTTTTTCCCTCTTGTGCTCAG
TCGCCCTGTTCTTGAGGTCTCTTTTCTCTACTCCATGGTTCTCAATTTATTTGGGGGGAAATACCTTGAGCAGAATACAATGGGAAAAGAGTCTCTACCC
CTTTCTGTTCGAAGTTCATTTTTATCCCTTCCTGTCTGAACAAAAACTGTATGGAATCAACACCACCGAGCTCTGTGGGAAAAAAGAAAAACCTGCTCCC
TTCGCTCTGCTGGAAGCTGGAGGGTGCTAGGCCCCTGTGTAGTAGTGCATAGAATTCTAGCTTTTTTCCTCCTTTCTCTGTATATTGGGCTCAGAGAGTA
CACTGTGTCTCTATGTGAATATGGACAGTTAGCATTTACCAACATGTATCTGTCTACTTTCTCTTGTTTAAAAAAAGAAAAAAAAACTTAAAAAAATGGG
GTTATAGAAGGTCAGCAAAGGGTGGGTTTGAGATGTTTGGGTGGGTTAAGTGGGCATTTTGACAACATGGCTTCTCCTTTGGCATGTTTAATTGTGATAT
TTGACAGACATCCTTGCAGTTTAAGATGACACTTTTAAAATAAATTCTCTCCTAATGATGACTTGAGCCCTGCCACTCAATGGGAGAATCAGCAGAACCT
GTAGGATCTTATTTGGAATTGACATTCTCTATTGTAATTTTGTTCCTGTTTATTTTTAAATTTTCTTTTTGTTTCACTGGAAAGGAAAGATGATGCTCAG
TTTTAAACGTTAAAAGTGTACAAGTTGCTTTGTTACAATAAAACTAAATGTGTACACAAAGGATTTGATGCTTTTCTCTCAGCATAGGTATGCTTACTAT
GACCTTCCAAGTTTGACTTGTATAACATCACTGTCAAACTTTGTCACCCTAACTTCGTATTTTTTGATACGCACTTTGCAGGATGACCTCAGGGCTATGT
GGATTGAGTAATGGGATTTGAATCAATGTATTAATATCTCCATAGCTGGGAAACGTGGGTTCAATTTGCCATTGGTTTCTGAAAGTATTCACATCATTTG
GGATACCAGATAGCTCAATACTCTCTGAGTACATTGTGCCCTTGATTTTTATCTCCAAGTGGCAGTTTTTAAAATTGGCCTTTTACCTGGATATAAATTA
ATTGTGCCTGCCACCACCATCCAACAGACCTGGTGCTCTAATGCCAAGTTATACACGGGACAGTTGCTGGCATGTCTTCATTGGCTATATAAAATGTGGC
CAAGAAGATAGGCTCTCAGTAAGAAGTCTGATGGTGAGCAGTAACTGTCCCTGCTTTCTGGTATAAAGCTCTCAAATGTGACCATGTGAATCTGGGTGGG
ATAATGGACTCAGCTCTGTCTGCTCAATGCCATTGTGCAGAGAAGCACCCTAATGCATAAGCTTTTTAATGCTGTAAAATATAGTCGCTGAAATTAAATG
CCACTTTTTCAGAGGTGAATTAATGGACAGTCTGGTGAACTTCAAAAGCTTTTTGATGTATAAAACTTGATAAATGGAACTATTCCATCAATAGGCAAAA
GTGTAACAACCTATCTAGATGGATAGTATGTAATTTCTGCACAGGTCTCTGTTTAGTAAATACATCACTGTATACCGATCAGGAATCTTGCTCCAATAAA
GGAACATAAAGATTT

Loop counts:

3 nts: 3
4 nts: 5
5 nts: 2
8 nts: 2

Tetra-loop variants:

GUAG    1
UUUU    1
GUCU    1
AUUU    1
UUUG    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: 1
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