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

AAGGGGGAGCTGCGGGCCAGGCGGCGGCCCCCTAGCGTCGCGCAGGGTCGGGGACTGCGCGGCGGTGCCAGGCCGGGCGTGGGCGAGAGCACGAACGGGC
TGCCTGCGGGCTGAGAGCGTCGAGCTGTCACCATGGGTGATCACGCTTGGAGCTTCCTAAAGGACTTCCTGGCCGGGGGCGTCGCCGCTGCCGTCTCCAA
GACCGCGGTCGCCCCCATCGAGAGGGTCAAACTGCTGCTGCAGGTCCAGCATGCCAGCAAACAGATCAGTGCTGAGAAGCAGTACAAAGGGATCATTGAT
TGTGTGGTGAGAATCCCTAAGGAGCAGGGCTTCCTCTCCTTCTGGAGGGGTAACCTGGCCAACGTGATCCGTTACTTCCCCACCCAAGCTCTCAACTTCG
CCTTCAAGGACAAGTACAAGCAGCTCTTCTTAGGGGGTGTGGATCGGCATAAGCAGTTCTGGCGCTACTTTGCTGGTAACCTGGCGTCCGGTGGGGCCGC
TGGGGCCACCTCCCTTTGCTTTGTCTACCCGCTGGACTTTGCTAGGACCAGGTTGGCTGCTGATGTGGGCAAGGGCGCCGCCCAGCGTGAGTTCCATGGT
CTGGGCGACTGTATCATCAAGATCTTCAAGTCTGATGGCCTGAGGGGGCTCTACCAGGGTTTCAACGTCTCTGTCCAAGGCATCATTATCTATAGAGCTG
CCTACTTCGGAGTCTATGATACTGCCAAGGGGATGCTGCCTGACCCCAAGAACGTGCACATTTTTGTGAGCTGGATGATTGCCCAGAGTGTGACGGCAGT
CGCAGGGCTGGTGTCCTACCCCTTTGACACTGTTCGTCGTAGAATGATGATGCAGTCCGGCCGGAAAGGGGCCGATATTATGTACACGGGGACAGTTGAC
TGCTGGAGGAAGATTGCAAAAGACGAAGGAGCCAAGGCCTTCTTCAAAGGTGCCTGGTCCAATGTGCTGAGAGGCATGGGCGGTGCTTTTGTATTGGTGT
TGTATGATGAGATCAAAAAATATGTCTAATGTAATTAAAACACAAGTTCACAGATTTACAGTGAACTTGATCTACAAGTTCACAGATCCATTGTGTGGTT
TAATAGACTATTCCTAGGGGAAGTAAAAAGATCTGGGATAAAACCAGACTGAAAGGAATACCTCAGAAGAGATGCTTCATTGAGTGTTCATTAAACCACA
CATGTATTTTGTATTTATTTTACATTTAAATTCCCACAGCAAATAGAAAATAATTTATCATACTTGTACAATTAACTGAAGAATTGATAATAACTGAATG
TGAAACATCAATAAAGACCACTTAATGCACGCTTTCTATTTTATTGAACTCTTATTAACTGTAAAATGCATTTTTAAAAGATCAAAAATGCATATTTTCT
AGCATGATTCATGTATCAGTCAGCAGCCAAGCTTCTAAATGCCAGATATTATATTGAGAATGTATTATATGAGAACGTACAATGCTTAAAGTTCCGGTTT
TCAAACTTAGGCAGGTCATATTCTATCTATCTTATCCAGCATTACTGTAGGCTAGAAAGTGATAATGGCTTTCATAATCCTGCCTTGTCTTAGGCACTTT
CCTGCAGTCTTTAGAAATTCTAAGATTCTGCTAAAAGTTTTAAATCACAATCTGGAGAATTTTCTATGATTAGGAAGTGCTCTGTTTTCATCCCTTTAGA
TAACTGTGACACCTAGAATTTTATGTTAAGTAGAGAGTATTCATTGAAAATCAAGGCCAGGTGCAGTGGCTCACACCTGTCACCCCAGCACTTTGGGAGG
CAGAGGTGGGCGTATCACTTCAGGCCAGGAGTTTGAGACCAGCCTGGCCAACCGAGCGAAACCCCATCTCTAATAAAAATACAAAAAATTAGCTGGGTGT
GGTGGCGCACACCTGTAATCCCAACTACTCAGGAGGCTGAGGCATCAGAATCACTTGAACCCGAGAGGCAGAGGTTGCAGTGAGCTGAGATGGCATGCCA
CCACATCCATCCTAAGCGACAGGGCAAGACTCTGTCTCAAAAAAAAAAAAAAGAAAGAAAATCAGTTGTCTTAGTTTAAGCTACTATAACAAGGTACTGT
AGACTGATGGCTTATAAGCAACAGAAACTTATTTCTCAGTTCTGTAGTCTGGAGGTCCAAGATCAAGGTGACACTGTGGTCAGGTTCTGATGAGGGCCCT
CTTCTGGGTTATAAACTACGGACTTCTTGTATCCTTACATGGCAGAAAGAGCGACAGAGCTCTCTGTAGTCCCTTTTATAAGCTCACTAATCCCATTCAT
GAGGGCCCTACCCTCATGACCCAATTACCTCCCAAATGCCCCTCCTCCAAACACCACCACTTTGGGGGTTAAGATTTCAACAGATGAATTTTGAAGGGAC
ACAAACATTCAGTCCATAGCATCACTTATCAAGCTAGTATTTAATACCTCTTAGGCCCCGTGGAAGGGAAAATAGATAGGAACCTGCCCTGAAAGATGCT
TCAGTTGGGGAGAAAAGGTGAAATTCCATTGTTAGACAATTTGTTTAAGACAATACATCTTGCTTGAGAAGGAATAGAAGGGAAATGAAATGGGGGGAGG
GAGTGGTAGGAGATGGAGGCTTTGAAAGAAAATAACCAGATTTAGAAACATGGGTATAGAAAGCATCCTCCAGTACTTCTGTAACAATTTATCAAGACCT
ACAGGAAGTCAGTTTTGGATTTGCTCCTCCGAGATTTGCGAGCCAGAGGAAAATACTTAGACTATCAGGTTGGAAAGTTCACACTTGGACCAGGAAAAGA
CCAAGCAGTTGCTATAGTCTCCTGGATTGTGACTAATCTGGAGGAAGCAAGTCCCTGTATCCTTGGCAAAGCTTGAAAGGCAGGCAAATGTCTTCTCTGT
GTTTTCTGACAGGTGGTTGGGTGGTGGGGGTTGGTCTCTGTACCTCCTGTTCTTTACCTTGCTTACCAAGCCCTTCCACCGACTCACTCCTGCCTCCCCA
GCTAAAAATTGGCTGTGTTGCTTTTACCACAGTTACCAAGGTCTGAGTTTTATAAAATCCAGGATCACATCTGACCTCACCTGGTAGATATCTAGGCCAA
TAAAGTCTAAAGGGCTAAAAAGAAGGTACCTCTCCATCCTGTCTCCTCGAGGCCAGGCAGCACATGTGCAGTTAAGAGGCCTCCTGGATCCATTGTCCTC
CTGTTGCTTTTCGTTCTAAGTGATCCAAACTCTATTGCTGATAGGGAATAAAAGCAGGGCAGGCTAGTAGTGGGCAAGTGCTTTGATGGAGCGTATCTCC
AAGCAGGGCCCAAGTTTAGGAGGAGGAAGACCTGATACAATGAATGAACAGTGCGTCCTCCCAACCCAACCAAGAAGTGTAATTGTGTTCCGTCTTTAAC
CCTGGCATGGAATGGGGAGGGAAGAGGCATGGACATTTATTACATAGTGCACATTATCTACATTCTCTGCATGTGACCCAGATGTCAGCCCTTCCGCTTC
CTGCGAAGGTTACCTCTAATGCACGTTGCCCCAGGCCCTGCTGAGCTAGTTCCTCACCGCAGCTACTTAACTCACCATGAATTCCTAGAACCCTCAGCCT
CTGAGAGTGCTGGGATCTGGCGGGAGAACAGGCAGTACTTCCCTCACTAACCTACCCGCACGCCATACCATCATTGTGCAAAGCTGCCTCATGCTGGAAG
GTCTGGTTTACGTAAAAGTGACAAGTTGGAATTGAGCGTCCGACTCTCGGGTACCTGCCCCAGGCATTTCTCATCAGCCCCATTTCCCACACAGCTCTCT
CCTAGGCGCAGCCCTCCTTCACCACCACCACCCCCACCCCAATCACCTTTAGGTATTTTCTCCCCTAAAGCCTCACCTGTTGGCATTTTACATCTTTTTA
AGACCTTATTTTGTATTTTAAATGTATGAGAAAAATTATGGAGGATGATGCAAGATGAGTGAGTCCATAATGGTAATAATTGGACACTAAAAACAATGAA
AACTTGTCTCAAGTATTTGTGTTGAAATCTCAATTAACTGGGCGACTGCTCCCGTTCCATTTTATTCTGTAAAATATGTGGCATCCTTTGTGTTGAGGCG
GCATTTACTAAACACCCCCAAGGTGCAAGGCTGCAAGAGAATCGAGCGCCGCAAGGCGAGCTTATCTTCCACACCTGGTACAGTGCCCAGGACAGAGAAG
GTGTTTAGCAAGTTTCTGCTGAATGGAAGAGTGAGCGAGAAGGGAAAGTGCATCTAAAAAGCACAGGGAACCTACAAAATATTTGGGAAAGGGTTTCATC
AGTTCGGGTGAAATCTTGAACGTGCAAAGCACCATGGGGGTGGCTGGACAGGCTTGTTGGAGTCGTATAATGCAATGAATAAAAACTTACGGCTGCCTTA
AATGCAAATGTCAAGCCCTTAAATAAAATTTAACAAAGTC

Loop counts:

5 nts: 2
7 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