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

TTTTAGCAGAGACATGGTTTCACCATGTTGATCAGGCTGGTCTCAAACTCCTGACCACAAGTGATCTGCCCGCCTCAGCCTCCCAAAGTGCTAGAATTGC
AGCATGAGCTACCGCGCCCACTCCTGGTTTTTTTATTTTTATTTTTTTAACATCCTTGAAGAAGTCATAATACATTTAAAACATTTGTCTTTGTAAGTAA
ACTGAAACCTCCTGCCACCTGTGGCTATAGGGAAAACTCGAGCTGGGTAGGACCAGAACCATATGAGTGGTAGAAGGAGAAAGATGCCTGGGCCTGGGCT
GAACTTAGGTTGTGGTCTCAGACCTAGGATCCAGGGGCCAAGTTTCCAAGCTTGCCCATCAGGAAGGTGGAGCGGTTAAGAACTCATATGCTAAATGCCA
CCCAGTGAAGGCCAACAGAGACCTCACTGCCCCTGCTTCTGGGCAGCAGCTATAGTGACCATTGGGGCCATCACAACGTTTAGACAGGTTTGTGCAGCAG
CACATTCCTCCCCTGGGCCTTTGACTGGATGTGCACCAGATTTCCTGCCAGCCTGACTGTCTTGCTTGGATCTGCAGAGAGCCTGTTACCTATCCATAAA
CCCCCAAAAGGATGAGACGCTAGAGACAGAGAAAGCTCAGTACTACCTGCCTGATGGCAGCACCATTGAGGTAGGTGGCCTGCCTTCTTTCTTCGGTCCC
CTTAGGTCCACAAAAGCTCTGGGCCCAACCAGAATTCTCCATCAGGGTCTGGAGTCTGGCAGGCCAGTCCCTTTACACCAAGCTTGTCCAACCCCTGGCC
CATGGGCTGCACGTGGCCCAGGATGGCTTTCAGTAAGGCCCAACACAAAGTCGTAAACTTTCTTAAAACATTATGAGATTCTTTTGCAATTTTTTTTTTT
AGCTCAGCAGCTGTCATTAGTGTTAGTGTATATTATGTGTGGCCCAAGACAATTCTTCTTCCAATGTGGCCCAGGGAAGCCAAAAGACTGGACACCCCAG
CCTTACACCCTCTCTCTGGAGCAGCAGAGCTCCTGAGCATGAGTGGCCCTGTCTCCTGCAGAGGAGGCAGCCAGAACTTTGCTCCCTCCCGCTAGAGGGG
AGGAAGCTCCTAAGGGATTGTCCCACATCAGTATGAGATTAGGAAGTGGGATGGTTAGTGCCATCCTTCACCACACCTGGGTGCAGTGTAGGGTGAGTTA
CCACTCCCTTGAACCCCCATTGCTAGGAAGACGTTTCCATGAGCAAATAAATCCATGTACTGATGCCAAAGACCTCTTGGCTGGAAAATGCCAGAGCGAG
AAGGAAATATAGGAGCCTCCCCTCACTAGTTTCCAGGAGGCCTATCTTTGTTCCTTTAAGCCCTTGACATGTAGAGTCTGTCTTGAGCCTGGCCTTCATA
GCCACCCAGTTACTAAGTGACGTGCAGAGGGGCGTCTTCCATTCCCACTCCCAAAGGGACCTTGGTCCCAGCTCCGACCTCTTCAGCTGGCCCTCCTACC
TGCAGATTGGTCCTTCCCGATTCCGGGCCCCTGAGTTGCTCTTCAGGCCAGATTTGATTGGAGAGGAGAGTGAAGGCATCCACGAGGTCCTGGTGTTCGC
CATTCAGAAGTCAGACATGGACCTGCGGCGCACGCTTTTCTCTAACATTGTCCTCTCAGGAGGCTCTACCCTGTTCAAAGGTTTTGGTGACAGGCTCCTG
AGTGAAGTGAAGAAACTAGCTCCAAAAGATGTGAAGATCAGGATATCTGCACCTCAGGAGAGACTGTATTCCACGTGGATTGGGGGCTCCATCCTTGCCT
CCCTGGACACCTTTAAGAAGATGTGGGTCTCCAAAAAGGAATATGAGGAAGACGGTGCCCGATCCATCCACAGAAAAACCTTCTAATGTCGGGACATCAT
CTTCACCTCTCTCTGAAGTTAACTCCACTTTAAAACTCGCTTTCTTGAGTCGGAGTGTTTGCGAGGAACTGCCTGTGTGTGAGTGCGTGTGTGGATATGA
GTGTGTGTGCACATGCGAGTGCCGTGTGGCCCTGGGACCCTGGGCCCAGAAAGGACGATGAACTACCTGCAGTGGTGATGGCCTGAGGCCTGGGGTTGAC
CACTAACTGGCTCCTGACAGGGAAGAGCGCTGGCAGAGGCTGTGCTCCCTCCTCAGGTGGCCTCTGGCTGGCTGTGGGGGACTCCGTTTACTACCACAGG
GAGACAGAGGGAGGTAAGCCATCCCCCGGGAGACCTTGCTGCTGACCATCCTAGGCTGGGCTGGCCCCACCCTCACCCCCACCCCCAGGGTGCCCTGAGG
CCCCAGGCAGCTGCTGCCTCCACTATCGATGCCTCCTGACTGCACACTGAGGACTGGGACTGGGGTTGAGTTCTGTCTGGTTTTGTTGCCATTTTGGTTT
GGGAGGCTGGAAAAGCACCCCAAGAGCTATTACAGAGACTGGAGTCAGGAGAGAGCAGGAGGCCCTCATGTTCACCAGGGAACAGGACCACACCGGCCAC
TGGAGGAGGGCAGGAGCAGTCCTCACTCTGAATGGCTGCAGAGTTAATGTTCCCAGCCCAGTCCCCTTTCGGGGGCCTTGGGAGAGTTTAAGGCACCTGC
TGGTTCCAGGACCTCGCTTTCCATCTGTTCTTGTTGCAATGCCATCTTCAAACCGTTTTATTTATTGAAGTGTTTGTTCAGTTAGGGGCTGGAGAGAGGG
AGCTTGCTGCCTCCTGCCTTGCTACACTAATGTTTACAGCACCTAAGCTTAGCCTCCAGGGCCCCACCTCTCCCAGCTGATGGTGAGCTGACAGTGTCCA
CAGGTTCCAGGACCATTTGAGATTGGAAGCTACACTCAAAGACACTCCCACCAGGCTCTTTCTCCCTTTTCCTCTTGCTCACTGCCCTGGAATCAACAGG
CTGGTTGCTGGTTAGATTTTCTGAAACAGGAGGTAAAATTTTTCTTTGGCAGAGGCCCCTAAGCAAGGGAGGGGTGTTGGAGAGCCAGTGCCCTTAAGAC
TGGAGAAAGCTGCAATTTACCAAGTTGCCTTTTGCCACTGTAGCTGACCAGGGGACTAGGTTGTAGAGGTGGGAAGGCCCCCTCTGGGCTGATCTTGTGC
CATTCTTGACCTTGGACCTGCTTGGTTAAGGAGGGAGTGGGCCAGACCAGAGTGCCAGGAGCTAATGGAGCCAGGCCTGACTCCTAGGAGTGGTCCAAAG
GCCTTCAGCCTAGATGGTGCAAAGCTGGGGCCAGCCTGTCTTCACCGGCACCCTCACCTGTGACACCAAGACCCACCCCAATCCCAGACTTCACACAGTA
TTCTCCCCCACGCCGTCCTATGACCAAAGGCCCCTGCCAGGTGTGGGCCACAGCAGCAGGTATGTGTGAAAGCAACGTAGCGCCCCGCGGACTGCAGTGC
GCTTAACCAACTCACCTCCCTTCTCTTAGCCCAAGCCTGTCCCTCGCACAGCCTCGCACAAACCACATTGCCTGGTGGGGCCCAGTGTACTGAAATAAAG
TCGTTCCGATAGACACGTC

Loop counts:

3 nts: 1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 0
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: 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