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

ACTTCCGCGGGCGCGTGCGCAGTGGCGGGCCGGGCGCGTGCGCAGCGCCGGCTTCTTCCCAGCGCGAGTTGCTGCTAACGCTCCTCCTCCAGCTTCCCAC
CCCCGCCGCCCGCCGCGGCCCGGTACCAACGGGTGGTCTCGCCGAGGGAGCTGTCGTGCCTCGTGGTCCCGGGACTGCAGTGGTGTGCGCTCTCGGCGCG
TGGCGCTAGGCATGGCGATGGATCAAGTAAACGCGCTGTGCGAGCAGCTGGTGAAAGCGGTGACGGTCATGATGGACCCCAACTCCACCCAGCGCTACCG
GCTGGAAGCCCTCAAGTTTTGTGAGGAGTTTAAAGAAAAGTGTCCTATCTGTGTCCCCTGTGGCTTGAGGTTGGCTGAGAAAACACAAGTTGCCATCGTC
AGACATTTTGGCCTTCAGATCCTGGAACACGTTGTCAAGTTTCGGTGGAACGGCATGTCTCGATTGGAGAAGGTGTATCTGAAGAACAGTGTCATGGAGC
TGATTGCAAATGGAACATTGAACATTTTGGAAGAGGAGAACCATATTAAAGATGCTCTGTCTCGAATTGTAGTGGAAATGATCAAGCGAGAGTGGCCACA
GCATTGGCCTGACATGCTAATAGAATTGGACACTCTTTCCAAACAAGGGGAAACACAGACAGAATTGGTGATGTTTATCCTTTTGCGACTGGCAGAGGAT
GTAGTGACTTTTCAGACACTTCCCCCTCAAAGAAGAAGGGACATCCAGCAAACATTAACCCAGAACATGGAAAGGATCTTCAGTTTTCTGCTTAACACAC
TTCAAGAAAATGTAAACAAGTATCAGCAAGTGAAGACAGATACTTCTCAGGAGTCAAAGGCGCAAGCAAACTGTCGAGTAGGAGTTGCAGCACTGAATAC
TCTAGCAGGCTATATTGACTGGGTGTCTATGAGTCACATCACTGCTGAAAACTGTAAACTCCTGGAGATACTGTGTTTGCTGTTGAATGAACAGGAACTT
CAGTTGGGAGCCGCTGAGTGTCTTCTCATTGCAGTCAGCAGAAAAGGCAAGTTGGAAGACCGGAAGCCCTTGATGGTCTTATTTGGAGATGTTGCCATGC
ATTATATACTCTCCGCCGCACAGACTGCTGATGGAGGAGGTTTGGTAGAAAAACACTACGTCTTTCTGAAGAGGCTCTGTCAGGTGTTGTGTGCGCTGGG
CAATCAGCTGTGTGCATTGCTGGGTGCAGATTCTGATGTAGAAACACCATCAAACTTTGGAAAATACCTGGAATCTTTTCTTGCTTTCACAACCCATCCA
AGTCAGTTTCTACGCTCTTCAACTCAGATGACTTGGGGAGCCCTCTTCAGGCATGAAATCCTGTCCCGTGATCCTTTGCTATTAGCAATAATACCAAAAT
ATCTTCGTGCTTCCATGACTAACTTGGTCAAGATGGGCTTTCCTTCTAAAACAGACAGCCCTAGCTGTGAATATTCTCGGTTTGATTTTGATAGCGATGA
GGACTTCAATGCTTTCTTCAACTCCTCCCGAGCACAACAAGGAGAGGTGATGAGGTTGGCATGTCGTTTGGATCCCAAAACTAGCTTCCAGATGGCTGGG
GAGTGGCTAAAGTATCAACTATCAACTTTTCTTGATGCTGGTTCTGTGAATTCTTGTTCTGCAGTTGGAACTGGAGAAGGAAGCCTCTGTTCCGTCTTCT
CACCTTCATTCGTGCAGTGGGAAGCCATGACTCTTTTTTTGGAAAGTGTTATCACCCAGATGTTTCGAACACTAAATAGAGAAGAAATTCCTGTTAATGA
TGGAATAGAGCTATTGCAGATGGTTCTGAACTTTGATACCAAGGATCCCCTCATCCTGTCCTGCGTCCTTACTAATGTCTCTGCACTCTTTCCATTTGTC
ACCTACAGACCAGAGTTCCTGCCCCAGGTCTTCTCTAAGCTATTTTCATCTGTCACTTTTGAAACTGTTGAAGAAAGTAAGGCCCCCAGAACCCGGGCAG
TGAGGAATGTGAGGAGGCATGCTTGTTCCTCCATCATCAAGATGTGTCGTGACTACCCCCAGCTTGTGCTGCCCAATTTTGACATGCTTTATAACCATGT
GAAGCAACTCCTCTCCAATGAGCTACTCCTGACACAAATGGAGAAGTGTGCCCTCATGGAAGCCCTGGTTCTCATTAGCAACCAATTTAAGAACTACGAG
CGTCAGAAGGTGTTCCTAGAGGAGCTGATGGCACCAGTGGCCAGCATCTGGCTTTCTCAAGACATGCACAGAGTGCTGTCAGATGTTGATGCTTTCATTG
CGTATGTGGGTACAGATCAGAAGAGCTGTGACCCAGGCCTGGAGGATCCGTGTGGCTTAAACCGTGCACGAATGAGCTTTTGTGTATACAGCATTCTGGG
TGTGGTGAAACGAACTTGCTGGCCCACTGACCTAGAAGAGGCCAAAGCTGGGGGATTTGTGGTGGGTTATACATCCAGTGGAAATCCAATCTTCCGTAAC
CCCTGCACAGAGCAGATTCTGAAACTTCTTGACAATTTGCTTGCGCTTATAAGAACCCACAATACATTATATGCACCAGAAATGCTAGCCAAAATGGCAG
AGCCTTTCACCAAGGCTCTGGATATGCTTGACGCGGAAAAATCTGCTATATTAGGATTACCTCAACCTCTCTTGGAACTCAATGACTCTCCTGTCTTCAA
AACCGTCTTGGAAAGAATGCAGCGTTTCTTCTCTACCCTCTATGAAAACTGTTTTCATATCCTAGGGAAGGCAGGCCCTTCCATGCAGCAAGACTTCTAT
ACTGTGGAGGACCTTGCTACCCAGCTTCTCAGCTCAGCCTTTGTCAACTTGAACAATATTCCTGACTACCGACTCAGACCCATGCTTCGTGTCTTTGTAA
AGCCTCTGGTGCTCTTCTGTCCCCCAGAGCACTATGAAGCCCTGGTATCCCCCATCCTCGGACCTCTTTTCACCTACCTCCATATGAGGCTTTCTCAGAA
ATGGCAAGTTATCAACCAAAGGAGCCTGCTGTGTGGAGAAGATGAGGCTGCAGATGAAAACCCAGAGTCTCAAGAGATGCTGGAGGAGCAACTGGTGAGG
ATGTTAACCCGAGAAGTCATGGACCTAATCACGGTTTGCTGTGTTTCAAAGAAGGGTGCTGACCACAGTAGTGCTCCCCCAGCAGATGGAGACGATGAAG
AAATGATGGCCACAGAGGTCACCCCCTCAGCTATGGCAGAGCTTACAGACCTGGGCAAATGTCTGATGAAGCATGAGGATGTTTGTACAGCGCTATTAAT
TACAGCCTTCAATTCCCTGGCCTGGAAAGATACTCTGTCCTGCCAGAGGACAACCTCACAGCTCTGCTGGCCTCTCCTCAAACAAGTGCTGTCAGGGACA
CTGCTCGCAGATGCAGTTACGTGGCTTTTCACCAGTGTGCTGAAAGGCTTACAGATGCACGGGCAGCACGACGGGTGCATGGCTTCCCTGGTCCATCTGG
CCTTCCAGATATACGAGGCACTGCGCCCCAGGTACCTGGAGATAAGAGCTGTAATGGAGCAAATCCCTGAAATACAGAAGGACTCACTGGACCAGTTTGA
CTGCAAGCTTTTAAACCCCTCCCTGCAGAAAGTGGCTGACAAGCGCCGAAAGGACCAATTCAAACGCCTCATTGCTGGTTGCATTGGGAAACCCTTGGGA
GAGCAGTTCCGAAAAGAAGTTCACATTAAGAATCTTCCCTCACTTTTCAAAAAAACAAAGCCAATGCTGGAGACGGAGGTGCTGGACAATGATGGGGGTG
GCCTGGCCACCATCTTTGAACCCTGAATCAAGCTTTTGGGCATCCTTCCTCGGCCTTTCTTGTCATCTCTTCTTTCCCTTTGTAGCCGATCTCTAGGCCC
TTCTTGCACTGCCACCTCACTTTCCACCACTGTCAGCCTGGAAAGAGATCCAGGTCTGGAGCTGGAGAGAACAGGCCCTGTGCAGGACCAGAAGTAATTA
TACTAAAGTATCAAGAAAGGGAGTTAGGGCTTAAACTATTCTGTCTAGATGTCCCAGATAGTTCCCATTCTACTTGGAGATTTGGCTTTTCCAAGAAAAG
CTAGAGCAGAGCAGCCCTTCTCCCACAAGCCCTCCCACCCCCGTGCAGCCACATACCTGTACAGAATGGTAACTAAGGGTGCTGTGCCCAACCCTGCGAC
TAGCAAGGCTCGCAGCAAGAGCACAGCCCTCAACTACTTGTGCCAGAGTTTCTCTTGGACCACTCCAACTCCCACTGAGCCCTTTTGCTGCTGGGCTGGC
AGGAAACTTTCCCCACTCCCTAAGGGGCATGTCTGGGTTAGGTGCTAAGTGCTGAAGAGAACTTGGTCAGTTCTCTCAACTTTGCTTTGGGCAAGAATCT
GGTCACCTGATGGGATCCATGGTACAGGCTACTGCTAAACTTGGCACAGTATCAAGTATAGTACCTCCAAGGACCAGGGCTGGGAAGTCTTTAGTGCTAA
CATCCCCTTTAGAGTTCACACATCTTGCCCTTCCATGAATGACCCCTCAGTCTGGCCTCCCCAGCCTCAAGGTCCACTCAGGCACAAGAGCCACAGTACC
CTAGATAGTGTCACATGACACCGTTGTCATCCAAGGATAATACAGACCAACTAGGCTACATCTGTGATGAGCAGCTAGCAAAGCCGCTGGTCTTCTCCTA
GGACTAAGTCCAGGTGCCTTCCACAATCTCATGGTCTTTCAGGTCCCTGGTTACTTTTCTCAAAGGCCATTTCCAAAAGAATACATGCCTTCACATCACA
ACCTGTACTGTGAGTCCATTCTAGAGGTCACTGAAAGGCCCTGTAAAGAGAGGACATGGATACGGGACCTGGCCCTGAGGTTATTACTGGCCGTAAGGCA
GAGTTAATCCATACAGAAACCAGTGTGTCCATGTGCTCTGCACAAAAACAGACCTGTTGTCCATCCAGTCCACTGACAAGAGGGTTTCCCCGAGAGCCGA
AGTGGACTGAAGCTACAGTTTTTAGCTGGTGCGGGCCACAGGCAGGGTCAGATTGAGAAGAAGCAAAGCTGGGGAAGCAGAAGTTGGGAGTCTTGTGTTG
CTCCCTCTTCCTGTGTGGTGCTCTGGGTTTCTGTGGATCGTGAAGGCGATCTCAAGAGTGTTTCCCTCCAAACCTGATAGCTGCCTATTCCTGTCTGGTT
GGGGCTGTGGAGGATGTAGTTGTATTTATTGCATTGTAATATTTTTAACATCCTGTGACTTCATGCTAGAAATTTTCTATTGTTTATAGAAACTTTTTGT
AGAAACATTAACTCTAAAGCACATCTGCATGTCAGTAAAAATCTCAGTTTCGTACAGAAAGGGA

Loop counts:

5 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: 1
C x G bulge: 0
C x A bulge: 0
C x U bulge: 1
C x C bulge: 0