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

CGGAGCCGAAACACCGGTAGGAGCGGGGAGGTGGGTACTACACAACCGTCTCCAGCCTTGGTCTGAGTGGACTGTCCTGCAGGTAAAGTACTTCTCTTCC
TGGTCAGGTTGTCACGCTCTTACTTCCTGCCTTGTCCGCGAGCGCCTGGAAAATAGAGGCCTTGAGCCCGAGCGGCGAAGTCCGGGCTTGAAGCTGCCGC
TGGGAGATTTCTCTTGCTGTCACCCCTCCCCCCTCGGCCGCTCCCCGGCGGCCCGGGCTCCCGCGCGCAGCTCCCGGGCGCCACTTTTCCAAGCTACTCA
AATGTCTCGGGGAGGCCCTGAGCCTCGCAGATCTTTTCTTTAAAAAATCCTAGTCTCTATCTGGAAAAGGGCGTCTCCCCCTACCCCTCTTCCTTCTGCC
AACGGACTAGTCACCGGGTCTCAGCCTTCGCTGGTGACCTTTCATGGTTTACTGTCCAACGGGACTCCGCCTGGGGAGCTGGAGAGACAAACTCTTGCCA
CTCCAAAATTAGCAAGCGCTGCCAGCGTCCGACTTGAAGTTGCTAGTGGTTAGTCCCAGCCTTCGCCCTTCGCGGTCCGACCGCTGAGAGGAGGGAGACT
TCGTTATGCCCCGGGCCGTCAACGGCGCCAGGAGCTAAAGGGCGGGCAGACGAAAGCGGGCGGCGAGTCGCCAGTTAGTCTTCACCGCTCTGGAGAGAGT
TGCTAGCCACGGGATCCTGACCCGGACACGAACTCGTTTCTCCACGTCGGTGCGCGCTTGCATCCCTGGCCCCGAAAGCGTGGGAATGTCCGGAAATGCT
GGCGTATGGGAGTTCCTTAATTAGAAATGCGTTAGCGAATATTATACGCTTATACTATGGGCGGACGGGTGGAGAGCCTTAAAAACAACAACAACAAACT
AAGCAGTTGCTCAATCGTTGATTGATCCTCAGGCACGTCTAGATTTTCCCACTTACATAGGTCTTGTTAAGAAACCAGTCCTGCCTTCTTGCCACTCGTG
TCTTTCGATGGCTCCCTTCCCGAAGTCCCGCTGCCTCTAAGCGGAGTGTTAAGCGGGGCTCTCGGAAGCCGGTGGACCGAGATTTCCCCGGGTGGGGCGG
GCGCGGTGTAGCGGCCCGCGGGCTGACTTGCTCCCGGCTGTCCCCCGGCCCCAGCGACCATGCCCCGTAAAGGCACCCAGCCCTCCACTGCCCGGCGCAG
AGAGGAAGGGCCGCCGCCGCCGTCCCCTGACGGCGCCAGCAGCGACGCGGAGCCTGAGCCGCCGTCCGGCCGCACGGAGAGCCCAGCCACCGCCGCAGAG
ACTGCAAGTGAGGAACTTGATAATAGAAGTTTAGAAGAGATTTTGAACAGCATTCCTCCTCCCCCGCCTCCAGCAATGACCAATGAAGCTGGAGCTCCTC
GGCTTATGATAACTCATATTGTAAACCAGAACTTCAAATCCTATGCTGGGGAGAAAATTCTGGGACCTTTCCATAAGCGCTTTTCCTGTATTATCGGGCC
AAATGGCAGTGGCAAATCCAATGTTATTGATTCTATGCTTTTTGTGTTTGGCTATCGAGCACAAAAAATAAGATCTAAAAAACTCTCAGTATTAATACAT
AATTCTGATGAACACAAGGACATTCAGAGTTGTACAGTAGAAGTTCATTTTCAAAAGATAATTGATAAGGAAGGGGATGATTATGAAGTCATTCCTAACA
GTAATTTCTATGTATCCAGAACGGCCTGCAGAGATAATACTTCTGTCTATCACATAAGTGGAAAGAAAAAGACATTTAAGGATGTTGGAAATCTTCTTCG
AAGCCATGGAATTGACTTGGACCATAATAGATTTTTAATTTTACAGGGTGAAGTTGAACAAATTGCTATGATGAAACCAAAAGGCCAGACTGAACACGAT
GAGGGTATGCTTGAATATTTAGAAGATATAATTGGTTGTGGACGGCTAAATGAACCTATTAAAGTCTTGTGTCGGAGAGTTGAAATATTAAATGAACACA
GAGGAGAGAAGTTAAACAGGGTAAAGATGGTGGAAAAGGAAAAGGATGCCTTAGAAGGAGAGAAAAACATAGCTATCGAATTTCTTACCTTGGAAAATGA
AATATTTAGAAAAAAGAATCATGTTTGTCAATATTATATTTATGAGTTGCAGAAACGAATTGCTGAAATGGAAACTCAAAAGGAAAAAATTCATGAAGAT
ACCAAAGAAATTAATGAGAAGAGCAATATACTATCAAATGAAATGAAAGCTAAGAATAAAGATGTAAAAGATACAGAAAAGAAACTGAATAAAATTACAA
AATTTATTGAGGAGAATAAAGAAAAATTTACACAGCTAGATTTGGAAGATGTTCAAGTTAGAGAAAAGTTAAAACATGCCACGAGTAAAGCCAAAAAACT
GGAGAAACAACTTCAAAAAGATAAAGAAAAGGTTGAAGAATTTAAAAGTATACCTGCCAAGAGTAACAATATCATTAATGAAACAACAACCAGAAACAAT
GCCCTCGAGAAGGAAAAAGAGAAAGAAGAAAAAAAATTAAAGGAAGTTATGGATAGCCTTAAACAGGAAACACAAGGGCTTCAGAAAGAAAAAGAAAGTC
GAGAGAAAGAACTTATGGGTTTCAGCAAATCGGTAAATGAAGCACGTTCAAAGATGGATGTAGCCCAGTCAGAACTTGATATCTATCTCAGTCGTCATAA
TACTGCAGTGTCTCAATTAACTAAGGCTAAGGAAGCTCTAATTGCAGCTTCTGAGACTCTCAAAGAAAGGAAAGCTGCAATCAGAGATATAGAAGGAAAA
CTCCCTCAAACTGAACAAGAATTAAAGGAGAAAGAAAAAGAACTTCAAAAACTTACACAAGAAGAAACAAACTTTAAAAGTTTGGTTCATGATCTCTTTC
AAAAAGTTGAAGAAGCAAAGAGCTCATTAGCAATGAATCGAAGTAGGGGGAAAGTCCTTGATGCAATAATTCAAGAAAAAAAATCTGGCAGGATTCCAGG
AATATATGGAAGATTGGGGGACTTAGGAGCCATTGATGAAAAATACGACGTGGCTATATCATCCTGTTGTCATGCACTGGACTACATTGTTGTTGATTCT
ATTGATATAGCCCAAGAATGTGTAAACTTCCTTAAAAGACAAAATATTGGAGTTGCAACCTTTATAGGTTTAGATAAGATGGCTGTATGGGCGAAAAAGA
TGACCGAAATTCAAACTCCTGAAAATACTCCTCGTTTATTTGATTTAGTAAAAGTAAAAGATGAGAAAATTCGCCAAGCTTTTTATTTTGCTTTACGAGA
TACCTTAGTAGCTGACAACTTGGATCAAGCCACAAGAGTAGCATATCAAAAAGATAGAAGATGGAGAGTGGTAACTTTACAGGGACAAATCATAGAACAG
TCAGGTACAATGACTGGTGGTGGAAGCAAAGTAATGAAAGGAAGAATGGGTTCCTCACTTGTTATTGAAATCTCTGAAGAAGAGGTAAACAAAATGGAAT
CACAGTTGCAAAACGACTCTAAAAAAGCAATGCAAATCCAAGAACAGAAAGTACAACTTGAAGAAAGAGTAGTTAAGTTACGGCATAGTGAACGAGAAAT
GAGGAACACACTAGAAAAATTTACTGCAAGCATCCAGCGTTTAATAGAGCAAGAAGAATATTTGAATGTCCAAGTTAAGGAACTTGAAGCTAATGTACTT
GCTACAGCCCCTGACAAAAAAAAGCAGAAATTGCTAGAAGAAAACGTTAGTGCTTTCAAAACAGAATATGATGCTGTGGCTGAGAAAGCTGGTAAAGTAG
AAGCTGAGGTTAAACGCTTACACAATACCATCGTAGAAATCAATAATCATAAACTCAAGGCCCAACAAGACAAACTTGATAAAATAAATAAGCAATTAGA
TGAATGTGCTTCTGCTATTACTAAAGCCCAAGTAGCAATCAAGACTGCTGACAGAAACCTTCAAAAGGCACAAGACTCTGTCTTGCGTACAGAGAAAGAA
ATAAAAGATACTGAGAAAGAGGTGGATGACCTAACAGCAGAGCTGAAAAGTCTTGAGGACAAAGCAGCAGAGGTCGTAAAGAATACAAATGCTGCAGAGA
TTTCAAAAATATCACTGCATCCTATAGAAGATAATCCTATTGAAGAGATTTCGGTTCTAAGCCCAGAGGATCTTGAAGCGATCAAGAATCCAGATTCTAT
AACAAATCAAATTGCACTTTTGGAAGCCCGGTGTCATGAAATGAAACCAAACCTCGGTGCCATCGCAGAGTATAAAAAGAAGGAAGAATTGTATTTGCAA
CGGGTAGCAGAATTGGACAAAATTACTTATGAAAGAGACAGTTTTAGACAGGCATATGAAGATCTTCGGAAACAAAGGCTTAATGAATTTATGGCAGGTT
TTTATATAATAACAAATAAATTAAAGGAAAATTACCAAATGCTTACTTTGGGAGGGGACGCCGAACTCGAGCTTGTAGACAGCTTGGATCCTTTCTCTGA
AGGAATCATGTTCAGTGTTCGACCACCTAAGAAAAGTTGGAAAAAGATCTTCAACCTTTCGGGAGGAGAGAAAACACTTAGTTCATTGGCTTTAGTATTT
GCTCTTCACCACTACAAGCCCACTCCCCTTTACTTCATGGATGAGATTGATGCAGCCCTTGATTTTAAAAATGTGTCCATTGTTGCATTTTATATATATG
AACAAACAAAAAATGCACAGTTCATAATAATTTCTCTTCGAAATAATATGTTTGAGATTTCGGATAGACTTATTGGAATTTACAAGACATACAACATAAC
AAAAAGTGTTGCTGTAAATCCAAAAGAAATTGCATCTAAGGGACTTTGTTGAACTTTATGCTGAAGATTCTTCAAGTTGATTCAGTGTATTACTGATTTT
TTTCTATTTGTAAAGGATTATGAGTTGTATAAAATACATACTCCCTAAACTAGATCATGAAACTGGTTTCTGTTTTATGCAGTTGTCATTTGTAAAGTCT
AATAAAATATTCTCTATAATTGCTTCTAGATTA

Loop counts:

3 nts: 3
4 nts: 1
8 nts: 1

Tetra-loop variants:

UGUU    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: 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