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

AGGGGTCGGAGCGCGGGGGCCGGCCGAGAGGAAAGCTGGAGGCGCGGGTGGGGAACATGTCTGAGTCGGAGCTCGGCAGGAAGTGGGACCGGTGTCTGGC
GGATGCGGTCGTGAAGATAGGTACTGGTTTTGGATTAGGAATTGTTTTCTCACTTACCTTCTTTAAAAGAAGAATGTGGCCATTAGCCTTCGGTTCTGGC
ATGGGATTAGGAATGGCTTATTCCAACTGTCAGCATGATTTCCAGGCTCCATATCTTCTACATGGAAAATATGTCAAAGAGCAGGAGCAGTGACTTCACC
TGAGAACATCCCAGCGGGAGGACAAGAGAAATCATGTTTATTCCTCAGGAATACTGAAGTGCCCTGGAGTAAGCTGCCATTCTTCTGTAACAATGTTATC
AGTAATGCTTTAAACTCCAGCACCTGGTTATGCATTTGAAACCAAGTCTGTTTCTTGTTTTGTATTTTCTCTCTGGAAGTTGTAAGGAGGTGGTCTTAAA
TAAATTAAACAAAAAGAGGAAGTCCATTGCATGGCCTTTGTTTCTTCACCTTTGGTCTCTGAGCATGAGGAGGACTGTGTGTGAACTGCCAGCAGCTGTA
GCCACCTGCTCACAGCCTCTCTGAGAACCCCCTGAAACCAGTTGTTGGGTATCCTTCCCATTTGCCCCCTCAGGCGTAGTTTTCAGAACTGCTTCCACCT
CGTAATCAGAAGTTGAAGATTGCTGCTGCGTGGCCTGATGGAGATGACTGATGTCTTAAGGCGCCTTTCCTTCTGTGGCACCTCTTCGTGTGTTCTCACC
TGGGGACCTGGCAGGGCACATCTCCGCTGTGCCTACTGCAAGGCGGTCCCACTGCTGCTGTATTAGCAGGGGAAGAATCCTGGCTGTGTGGATGGCCCAC
TCCATTGAAGTCAAGTCCTGCAGCTTCATAGAGCTTGAGACAGTCCAAGCTTCAGCTCTGGAGGGCGGAGGAAAGCTCATGGCATACCCACCTGGCCGGA
GGAGCCCGATTGGGGTTAATTTTATCTTCACGTAGCAGCTGAAGTTTGAGGACAAAAGGGCCACTTCTGATGCCCCTCTGAGTTTGTTCCTGTGGTTTCA
CTTGAACCAGGGATGCTAGATGCAAAAGTCATATTTTAGCAATTTCTTCAGACGATATACAGAACCCCAGCGCTCAGCCGTTCTTATTTCTTTTTCCTTA
TCGTAGAATTAAGATAGGGAGAGCCCGATCCCACTTGCCCCTGTATCCTGTAAATGTTGATTTATCATCTACTGTAAGCGAGGCACTGTTGTAAGCAGCA
GAGATAAATGGATAAATAGACACAGGCTTCTGCCTTCAAGGAGCTTAGAGTCTGATGGAAAGACAGACGTGCAAACACAACTCTGAAAGAAGTGTTTTAA
TGGAGAAGAGAGGTGTAGGCAAAGTACACTGAGAACAAAGGAGAAGGAGCAACTATGTCTCCCTAGGATGGCCCCACAGGCGACGGAATGCCTGCGCTGG
GACCCGAAGTTGACTGGGAATCCCAGACAGAAGGAGGGTAGCCTCTGTGTTTGCTCAGGATCATGTAATGCATATTATAGCTGGGAAATCGCAAGTAGTT
CAGCATAGCCAGGGTGTGTAGGGGCAGGGGAAAGGCATGGAGGGGGAGGCTGGGCAATAGGGTACAACTCATGTCTGACTCCAGTTCTGGAACATTGATT
AGACCTTAGTTCTTGCAAGTGCTATAGTGAGTACATTCAGGGTAGCAAATACCCTCCCTCAGCCTCCCCACTCCCTTTTCCAGAAAGGTCTGCTAGGCTC
TGCCCTGCAAACTGTCCAGGCTCCTCTGCCCTCTGGGCTTGTTTTCCTCTTTATTGCTACTTGGCTGTTTTTCACTTGGTCCTCTTCATTCTATGATTAA
GGCAACCCATATAATTGAAAGAAAAATAATGTGCAGCCTGTTTCATCCCTTCCACTTGTTTTCTTACTATTTATTTATTTATTTCTGAGATGGAATTTTG
CTCTTGTTGCCCAGGCTGGAGTGCAATGGTGGCGATCTCGGCCTGCTGCAACCTCCGCTTCCTGGGTTCAAGCGCTTCTCCTGCCTCAGCCTCCCGAGTA
GCTGGGATTACAGGCATGCGCCATCACACCTGGCTAATTTTGTATTTTTAGTAGAGACGGTGTTTCTCCTTGGTCATGCTGGTCTCCAACTCCCGACCTC
AGGTGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGCCTCCTATTTGCTTTAAAAGTAATTTCCTGGCCGGA
TGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCATGAGGTCAAGAGATCAAGACCATCCTGGCCAACATTGTAAAACC
CTGTCTCTACTAAAAATATAAAAATCAGCTGGGCATGGTGGCGCACACCTGTAGTCCCAGCTACTCAGGAGGTTGAGGCAGGAGAATCATTTGAACCCGG
GAGGCAGAGGTTGCGGTGAGCTGAGATCGCGCCACTGCACTCCAGCCCGGCGACAGAGCGAGAATCTGTCTCAAAAAAAAAAAAAAAAAAAAAGCATTTT
CCTTCCCCAATTTTTCTGTCATTTTCCCATCCTCATTCAGGCAGAGAGAAGAATAACATGCCCCCTTCCAAAAAAGACAAAACACAAGGTAGCCACAAAT
TCCCTAGACACATTAGAAAAATAGGGAGTGGAGAGGGGCATTGGAATGAAAGTTCTCTATCTCATTAGCTGTTAGGCTTTAGGCATTTATTTGGATGGAT
CCCTTTGGCACCTTGGAAGCACCACTGAAGTGCTCTGAGAAAGGGGTCAGCTGTCTGAGGGAATAGTTCTGGATAGAGGCCACAGGAAGCACTGGCCAGT
TGCTTTAGTTCTAGATAGCTTTGTATTCCCGCCTTGTTGCCCTTAGCGGAGGCTGGCCCAAAGCACACTTGATCTTGTCCCCACTCCCTGCCCCCATCTC
AGATCAACCTTCAGAAAGTCCCGGCTTGTTGGCAAAGGCACACATTCTGTGTTACTCTTAAGTTTCATTAGAAATTCAAGTCCTCTGGGGCCCTGTTCCC
TTGTGGGCTTGTGCAACTGACTTTGTTTCTTGTCTGCCTTTCTGGAACCAAATCCAAGGAAATTCATGGGTTTGGGGAGACAGCGATGGGAACCCAGCAG
GGCACAGGATGCTAGGATAAAGCTGTGGCGCCCCAAAAGTGGCCTGCTCTGCCAACATACATAAATACATACAGTCTGAGCTTGACACTGTATAATTTGG
CCCAGAACAATATGTATTTTGAGCTCATTTAGGTGAATGACTTTGGCATTCCATGTACCCACTAGGGGAAGCTTTATCAGGCTGCATTTGCCTTATGCAG
AAGTATGCCTTTGTTCTGAGAAATGGCCTCAGAACACACTGTTGAGCTGTCTCCTTTAGTGAGTGTCATCCTCTCATCCATTTCAAAAGATTGCAGATGC
CGTCTTGAAGTCCTGCTTGTAAGAAATGCAGGGGTTGGGAATGGAGGAGATGACGATGTAGTTTTGCTTTTAGTTTTCCCAAACCTGTTTACATTTTTTA
AAAATGTAACCAACCCATAATTGCATTTTACTTGTCGTGGTTCGATCTGATTGTATTGTCGAAGGACTATTTTTGAACCTGTCCAAATAAACTCTGCAAA
GTATTTCCACAA

Loop counts:

3 nts: 2
4 nts: 1
5 nts: 2

Tetra-loop variants:

GAAA    1

Single bulge variants:

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