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

CTCCTTTCCGCTTCCGGTGTCCCCTACAGTCATGGCTGCCGCCGTCGCTGCTGCCGGTGCAGGGGAACCCCAGTCCCCGGACGAATTGCTCCCGAAAGGC
GACGCGGAGAAGCCTGAGGAGGAGCTGGAGGAGGACGACGATGAGGAGCTAGATGAGACCCTGTCGGAGAGACTATGGGGCCTGACGGAGATGTTTCCGG
AGAGGGTCCGGTCCGCGGCCGGAGCCACTTTTGATCTTTCCCTCTTTGTGGCTCAGAAAATGTACAGGTTTTCCAGGGCAGCCTTGTGGATTGGGACCAC
TTCCTTTATGATCCTGGTTCTTCCCGTTGTCTTTGAGACGGAGAAGTTGCAAATGGAGCAACAGCAGCAACTGCAGCAGCGGCAGATACTTCTAGGACCT
AACACAGGGCTCTCAGGAGGAATGCCAGGGGCTCTACCCTCACTTCCTGGAAAGATCTAGATTGTTATTGCTGTTTGAGCTGTCTCAGTGGGATAAGTTT
GAAATTCAAGTGTTTGAACTGCTGATAATTTGGATTTTTTTTTTTTTTTAACTTTGGCACATTGATCTATCTAAACCTGGTGGGGAGAATTATCCCCACA
TTGTCTCATGGAAAGACTCAACTTGCAACTGTGCCCTCCACACTATCCTTACTTCTGTCTCCACTCTGATACCAGAGTGCAGCCATGCAGATGGTTATTC
CAGCTCTGGTCACCCGACTCCTTTCACCAAATTGCTCCTAACTGGAAGATCTCACTTTCCCCTTGTGGGGTAGGAACCGATGCCAGTGGGAGGGATGTGC
CCCTGACCATTAACGACTGTTTTTTTTTTTTTTTTTTAAAGAATGGAGTTGTTGGGGCAGGACATGCACACAATGTGAAACAGACAAAATGCATTACACC
TGTAGTGTAAAGTGGCCACTATGAATCCCTATGTATGAGAGGAGGGAGGCAGGCTGCAGCTTCAGCCACAGAATGGGGACTATGGAAGACAGCAGGAGCT
CATTTCCTCTGCACATTTTGGCTGTTAGACCTGTGTGTGTGTTTAAAAAAAGAGAAGTCAGTGCTCACTTTTTGTATTTAAATATTAAAAATGATTCCAA
CTGAAAGTGTCATCCTAAGTACCTTGAAATGAGACCACGTCAGAGACATGTACTGCCCCTCACATTTTCTCACCTAAACCAGCAGCACCTCCATCTTAAC
AGCCATAGGCCCAAATTGTTTCCAAGTGAAAATTCATTTTTAGCCAAGTACTTCATAGCAATCTTTGCCCTGAATTTAGGCAGTCACTTTGAGATCCATC
AGCCTAAAACAAAGGATTGGGTCTATGTACTTCTTTAGTCTATAATGACACTGTGTAATTATAAAGTATTTGTAGGGAATAACATAGTACTGATTTCTGG
GGAATAGGGGAGGGGGACAGAATTTTTTTTTTTTTTTTTTTGCCTGAGATCAGGTCTCACTGGAGTACAGTGGTGTCGTTTGGGTTCACTGCAACCTCTT
ACCTCCCCTCCAACTTGGCCTCCTGGGTAGCTAAGACTACAGGTACACGCCACCGTGCCCAGCTAGTTTCTTTTATTTTTGGTAGAGTCAGGGTTTCGCC
TTGTTGCCCCAGATAGTCTTGAACTCCTGAGTTCTAGCCATCCACCCGCCTCTGGCCCCTCAAAGTGCTGGGATTATAGGCGTCACCCACCACGCCCAGC
CAGAGTAAGCCTTTTGTGTGTTTATCAGATCAACCAACACTACAATCTAGGTGGTACTGTTCCCATTTTACAGAAGAGGAAACAGCCACAGAAAGGTAAT
TGCTCAAGGCTGCAGAGTTAAGTGCTAGACCTGGATTCAAATCCAGGCAGTCCAGCTACAGAACACTGCTGCTGTGCGCTCGGGATGGTGGGGCTGGGCC
CAGGCCCGCTGGGTATACATGATCTTTCACTTGTTAACTAGGGAAAAACACTAGTCACCAGTGTGGTACAAACTTGTACTTAGGTGGATTCTTCAAATTG
TCAAGATTAGTTTTTATAAATTAAAATAGACTGAAAAATG

Loop counts:

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

Tetra-loop variants:

GCAG    1
UUGU    1
ACCU    1

Single bulge variants:

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

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: 2
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