Annotated gene sequence

Experiment = in vivo 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

CTCTTTCCGCCATCTTTCCGCGCCGGTGAGTAGCACTCTCTGAGAGCTCCAATTTCATCCGTCTGCCATCGGCGCCATCCTGCAATCTAAGCCACAATGG
TGCGCATGAATGTCCTGGCAGATGCTCTCAAGAGTATCAACAATGCCGAAAAGAGAGGCAAACGCCAGGTGCTTATTAGGCCGTGCTCCAAAGTCATCGT
CCGGTTTCTCACTGTGATGATGAAGCATGGTTACATTGGCGAATTTGAAATCATTGATGACCACAGAGCTGGGAAAATTGTTGTGAACCTCACAGGCAGG
CTAAACAAGTGTGGGGTGATCAGCCCCAGATTTGACGTGCAACTCAAAGACCTGGAAAAATGGCAGAATAATCTGCTTCCATCCCGCCAGTTTGGTTTCA
TTGTACTGACAACCTCAGCTGGCATCATGGACCATGAAGAAGCAAGACGAAAACACACAGGAGGGAAAATCCTGGGATTCTTTTTCTAGGGATGTAATAC
ATATATTTACAAATAAAATGCCTCATGGACTCTGGTGCTTCCACTTGGTCGTTTTGAGCCTTTACAGCAGTGTAGCCACAGCTTCTGCGGCAGCATGCAG
TTGCTTCGTTTATCGGTGAATGCGATTCCCTGAAGTGACTAATACAGCCAAGGGAAAAAGTTCTTATGAAACCAGTATGCCTAAGAAACAGTCACCCCTG
CTGTCTGCCAAAACCAGGTATTTGACACTAAATATTTTAGTTGTATTTCAGTTTTTTTTTTTTTTTTTCTTTTTTGGAGACAGAGTCTGACTCTATTGCT
CAGGCTGGAGTGCAGTGGCGCGATCTTGGCCCACTGCAACCTCCACCTCCCGGGTTCAAGTGATTGTCCTGTCTCAGCCGCCTGAGTAACTGGGATTACA
AGTGTGTGTCGCCACATCCGGCTAATTTTTATATTTTAGTAGAGACAGGGTTTCGCCATGTTGCCCAGGCTGGTCTTGAGTTCTGGGCCTCAAGTGATCA
GCCTACCTCGGCCTCCCGAAGTGCTGGGATTACAGCCACGAGCCATTACACCTGGCCTATATTTCAGTATTTTCTATTAGTTTTTGATGAATTTGTTTTG
CCTGGCTAGGATTATTCTGTAGATAGGATTTTAGATCTGGCTTTTGTCACTGACTGCTGTAATAAATACTTGCTAGGAATTTTTTTTTTTTTTTTTTTTT
TTTTAAGACAAAGTCGCTCTGTCACACAGGCTGGAGTGCAGTGGCATGATCTTGGCTCACTGCACCTCCGCTTCCCAGATTCAAGTAGTTCTCGTGCCTC
AGCCTCCTGAGTAGCTGGGATTACAGGTGTGTGCCACCATGTCTGGCTGATTTTTGTATTTTTAGTAGAGGTGGGGTTTCACCATGTTGGCCAGGCTGGT
CTCGAACTCCTGATCTCAAGTGATCTGCCTGCCTTGGTCTCCCAAAGTGCTGGGATTACAGGTGTGACCACCACGCCCTGCCTTAAGAATTGTTCCAAGA
GAATCTGGTGCCACTTGCAGGTGCCCATTGAAGTGCAATGGGCACTGTTGATCACTGAGGAGGTAGTGGGTGCTGACCCGGTGCTGGGGCCTGTCCCCTA
GTCTCTGCTTTGCCCTTGGCTAGCTAGGTGGTGTGCCAAGTGGGGAGAGAAGCTACCTTATTAAGGGGCATGGATCAGCTTCCTGAAAGGAGGGCCTGCC
TCTGTAAGATATGGGAAGTCGCTGAGAATGTTACAGAACGGCCCTAGAGATGGGGCAGATAACGGCCCCCATTTGTGAGAAGTGAGTTGGGAGGCATGTT
TGGGGCCTCTGATGTTTGGGAGGCTGTGGGTAATTAACATGAGTTTTGGGGTCCAGCAGCAGAATTCAGGTTTCCTCTTCCACTCAGTAACCTCAGCATC
CGTATCTGTAATGGGAATGATACAAAACCTATCCCCAAGTTGAGGGAAAAATGAGATTGTGTAAAGCGCACTTGGCACATGACAGTCACAAGCATGGGGA
CAGTGAGTCCAGAAGGATTTTCTTATGCCAGCATTGTAAGCCCTAGGATCACAGGGCTCTGGCTTGTTTAACCATCGTGTCTCTGGTCCCTAGCCTGCAA
ACCTGGTGTGTAGGGATGCCTCAGTCGCTTACATGTTGATTGAGTGAATCGTCGGTTTCTTTCTGGACACTGACTTCAAAAATAAAATAGGATATGAAAA
TGG

Loop counts:

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

Tetra-loop variants:

UCAA    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 2
U x 0 bulge: 1
C x 0 bulge: 2

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: 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