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

ACGAAGGAGAAGCAAACACTGCGCAGCGGGACCGTGCGCGGCCTCCGCTCCTGCGTGCGTGCGCTCGCTCGCGCGGGCTCAGTGCTGGCGCGTGAGGCGG
AGGCGGGCGGCGGCGGCGGCGCCTGCGCGGTCGGACTCGGTCGACGGTTCGCAGGGGAGGAGGCGGCGGGAGGCGGAGGAGGCGGCGGCGGCGATGGAGG
TGAAGCGGCTGAAAGTGACCGAGCTGCGGTCGGAGCTGCAGCGGCGGGGCCTGGACTCGCGCGGCCTCAAGGTGGATCTGGCGCAGCGGCTGCAGGAGGC
GCTGGACGCCGAGATGCTCGAGGACGAGGCCGGCGGCGGCGGGGCCGGGCCCGGCGGGGCCTGCAAGGCGGAGCCTCGGCCTGTGGCCGCGTCGGGCGGC
GGCCCGGGCGGGGACGAGGAGGAGGACGAAGAGGAGGAGGAGGAGGACGAGGAGGCGCTGCTTGAGGACGAGGACGAGGAGCCACCCCCTGCTCAAGCCT
TGGGTCAGGCCGCGCAGCCGCCGCCGGAGCCCCCGGAGGCGGCAGCCATGGAGGCCGCGGCCGAGCCAGATGCTTCCGAGAAGCCGGCGGAGGCCACGGC
CGGGTCAGGCGGGGTAAATGGTGGCGAAGAGCAGGGCCTCGGCAAGAGGGAGGAAGACGAACCCGAGGAGCGGAGCGGGGACGAGACGCCGGGATCCGAG
GTGCCGGGTGACAAGGCCGCCGAGGAACAGGGAGATGACCAGGATAGTGAAAAGTCAAAACCAGCAGGCTCAGATGGTGAGCGGCGGGGGGTAAAGAGAC
AGCGGGATGAGAAGGATGAACATGGCCGAGCTTACTATGAATTCCGAGAGGAGGCTTACCACAGCCGCTCAAAGTCTCCACTGCCTCCTGAAGAAGAGGC
AAAAGATGAGGAGGAGGATCAAACTCTTGTGAACCTGGACACGTATACCTCGGATCTGCATTTTCAAGTGAGCAAAGACCGCTATGGAGGGCAGCCACTT
TTCTCAGAGAAGTTCCCCACCCTTTGGTCTGGGGCAAGGAGTACTTACGGAGTGACAAAGGGAAAAGTCTGCTTTGAGGCAAAGGTAACCCAGAATCTCC
CAATGAAAGAAGGCTGCACAGAGGTCTCTCTCCTTCGAGTTGGGTGGTCTGTTGATTTTTCCCGTCCACAGCTTGGTGAAGATGAATTCTCTTACGGTTT
CGATGGACGAGGACTCAAGGCAGAAAATGGACAATTTGAGGAATTTGGCCAGACTTTTGGGGAGAATGATGTTATTGGCTGCTTTGCTAATTTTGAGACT
GAAGAAGTAGAACTTTCCTTCTCCAAGAATGGAGAAGACCTAGGTGTGGCATTCTGGATCAGCAAGGATTCCCTGGCAGACCGGGCCCTTCTACCCCATG
TCCTCTGCAAAAATTGTGTTGTAGAATTAAACTTCGGTCAGAAGGAGGAGCCCTTCTTCCCACCACCAGAAGAGTTTGTGTTCATTCATGCTGTGCCTGT
TGAGGAGCGTGTACGCACTGCAGTCCCTCCCAAGACCATAGAGGAATGTGAGGTGATTCTGATGGTGGGACTACCCGGATCTGGAAAGACCCAGTGGGCA
CTGAAATATGCAAAAGAAAACCCTGAGAAAAGATACAATGTCCTGGGAGCTGAGACTGTGCTCAATCAAATGAGGATGAAGGGTCTCGAGGAGCCAGAGA
TGGACCCCAAAAGCCGAGACCTTTTAGTTCAGCAAGCCTCCCAGTGCCTTAGTAAGCTGGTCCAGATTGCTTCCCGGACAAAGAGGAACTTTATTCTTGA
TCAGTGTAATGTGTACAATTCTGGCCAACGGCGGAAGCTATTGCTGTTCAAGACCTTCTCTCGGAAAGTGGTGGTGGTTGTCCCTAATGAGGAAGATTGG
AAGAAGAGGCTGGAGTTGAGGAAGGAAGTAGAGGGAGATGATGTGCCTGAATCTATAATGCTGGAGATGAAAGCCAACTTCTCTTTGCCTGAAAAATGCG
ACTATATGGATGAGGTGACATATGGGGAGCTGGAGAAGGAGGAAGCTCAGCCCATTGTCACTAAGTACAAGGAGGAGGCAAGGAAGCTTCTGCCCCCCTC
CGAGAAGCGGACAAATCGCCGAAACAACCGAAACAAGCGTAACCGGCAGAACCGAAGCCGGGGCCAAGGCTATGTGGGCGGGCAGCGCCGAGGCTACGAC
AACCGGGCCTACGGGCAGCAGTACTGGGGGCAGCCTGGAAACAGAGGGGGTTACCGTAATTTCTATGATCGATACAGGGGAGACTATGATCGATTTTACG
GGCGAGATTATGAGTACAACAGATACAGAGACTATTACAGACAATACAATCGGGATTGGCAGAGTTACTACTACCACCACCCCCAGGACAGAGACCGATA
CTACAGGAATTACTACGGGTACCAAGGGTATCGGTGAAGCCCCTGCCATGGTCACCTGTCAGCCATGAAGCTGAATCTCTGGGGGTGCCAGGCACCCCCG
CAAAACACAACCAAGGAAAACAGGGGCTGTCGGGGTGGGGCTGAGCTGCCGGGGAGGGGTGGTGGGGGGGGAGGGTGCTCAAGCAGGGGTGGGGGAGGGG
GGAGGTGGAAACAAACAACAAAACTGTACATTTTTTTTAAAGTTTGTTGAAAAGAATATTGTCTTATTCTATAAAACATTTCAAACCTAGTTAGAGATTT
GTAATCAAAAAACATTTGCGCAGAAAGCAGCACTTAGGGCTGCCTGTTCTATACCCTACAGTCAGACAGGAAAAGAACTGAAAATGGCACCCTTCTGACA
TTCTGAGGCAGCTGGACTGGCAGCCAAGTAAAGGAGAGTGATGAGGTGGTGTGGGGAGGGTGGGGAGGCAGCGCGAGGGTGCTCTCCACAGCAGGTAGGA
GCAGGCAGGAGTGGGGACAGAGGGAGAGCTTGTGACTGGGACAGTGAAAATAAACGATTGGCTCTTATCAATCACTTGCACCAACTAACCGTTTGTATTT
TCTTTACCGACCTTTCCCTTTTGGGATATGTGGTCTGGTGGGCTGGGAGGCTTACAGTGTCCCAACTCTCCATTTTCCTGTGCCTTTGTGCTGTTTGGCT
GAGGCATGGAGACTGCCAGTGGGTGGTTCTATTTTACAGGATTCCCAGGCCAAGAAAGCCTGGGGACTGTCCTTGATGGCAGAGCAGAATAGCCTGCCCC
TTCTATAGACCCATTGATTAATTCCTGTAAAATCTTGGGGAGAATGGGATTGCAGCCCTCAGCCTAAAGATTGTGATTTGCCAGTCTCTAGTCTCTGTCT
TCCAAGGTTGAGAGAGGTGGGAGGTCTCTGAAATCATCCCTGTTAGAGTGTCTGTCCTCTTACAGTGCGAGAGAAGGAACGTTTCTCAGGGTTTCAGCTC
ACACGAAAACACAGCAGGATTCTTTTCACTGCAGCGGGATATGTATATAGGTGAATCCTGTGGTGTGGGCTCACAGGCCCAGGTGCTGAGAATAGCAACT
AGCAACTATTTTCTACAGTGTGGAGGGCTCGTGCCCTGCTGGTTTTTTTGATACACAGGTAGAGAATGAATAGAAGAGGGGAGGGTGGTGGGGGGGGGTG
GGAGGCAGCTCAGTGGGGCTGCTGAACCTTGGGAAGAGTGTGAGTGTGAACGTGTGTAAATGTGCGTGTGAAAGGGAGCACCCCTTCCCGACTTCTAGAA
ACAAAATTCCTTTTGGGGCGCTTTCCCTGTGTGTCCCCAGAGAGGCCTCTAGCCAGGAGCCTTCAGTTGGGATAGTTTCATTTGTGACTTTACCAATACC
CTCCCAGTTCTTGATAGACAGCTGTAGGTTGCTGGGTTCAAGAATATGGGTGGGATATGGAATGCTCTTTCAATGTCTAGCTTCAGTTTTCATTCATCCT
CCTGCTCAGCACTGTCAGCCAAGAGCTTACTCAGCAGACACCACATACTGCAGCAGTTCCTAGTGAGAAAATCTGTGCCACTAGAAAATGCTTCACTTCC
ATTTCCTCACCTGGGCAGTTCTCTGTTTAAAATTGTGGGCTGATTTGGTCTTCCTCTCCTCCTCCCACTGTTACTGCCCTGCAGCCCTTGTTCAGGTGTA
CAGACCCTTATTCTGGCCTCTAGTGTCCTTGTCTGTCATGACACACCCTTCCGCCCAAATACCTCTGACCCCAAGGCTGGAATGGGGCTGGTAGGAGATA
AGTTTGCTTACTCATAGTCATGTCCTTTCTCTTGGCACCTGCTTCCCTGCGGTGTCCTCAAATGGATTTCTGTGTGGCAGTGGAGTGATTGCATGAATTT
TTCTGTAACACATTAACTTTGTATTATTATTAAGGGAGTTTGAGAAAGCTTTGCTTATAATGTCAAGGCAAGGAGGTAAAAACTGGAGCCCAAAGAAATT
CCCTTAGGGCAAGATTATGTTATAATAGAAAATTGAATTTCCTGAGGCAGTGGCTGCCACCCCTTTTCAGATGTTTAGTCCTGCAAATAGCATCTTTCTT
GTAGTCTGTGACATGGATGGGGATGCTAGGGCCCTTAGGGGCAAGGGGACTAAACTAAATCAAGTTGAGTTTTTTTCCAGCAGGGGTTAGGGGAGGTACT
CGCTGTTGATATTTGACACTAGAAAGTAATCTTTTTTACAAAACTGTTTTTCTAGGTGGGTGGAAAGTGAAACTGCCACATCCTTGTTGGTTTAGTCCAA
GAGATCATTTGCAACAACAGTAGATGTCCGGGTTTTGTTTCTGTCTTTTTATTATGAAAAACTATGTTAAGGGGGAAAATGTGGATTATGGTAACCAGAG
GAATCCCTAGCCTTGTTTTCCTTAGAAGACTTGTTTAGTGTTTTATCAGACGTCTGTTGTAGTTGTAGACAGGAAAGCTTGTGAGAAAAACACCACATGG
AGCCTGTAAATGTTTTTGCACAACCTGTAAAGCATTCTTGGAAGTGGCCAGTAAAAAGGGGTTTTACCATTTAAAAAAAAAATGTAACTGTGTCATTGTT
TACATCTGTAACTTTTTCCTCCCCTGTTCTCATTACACCATTCTGGCGAAAATGTAGGCAAAGTAGCTTCCAGTTTTAGAATAAATAACCATTTGGATTG
AATTCA

Loop counts:

3 nts: 1
4 nts: 1
6 nts: 1

Tetra-loop variants:

UAAU    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: 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: 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