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

GTCGCGTTGAAGCCAGCGTCCGGCCGGCAGAGCGGCGTCGGCGGGGTTGGCCGGGGCGGTGTGGCGCTAGAGCCTGGGCGGGCCGGGGGCAAGGAGTCAA
GGCTTGGGGGCGGGTGACGGGCGGGCGGAGGGCTTGCCCCCGTGTGGTCCTCGGAGCGGCCCGAGGTCCAGCCTCCCAGCGGTCCCGGAGGAGGATGCGA
CCGGGGGGCCCCGGGCGGGGCGGTCGGCGGCGGCTGCAGCGCTAGCGGCGCGGGGGCTGGGCGGCGGCGCCGGCATGAGGCGCAGGGCCGGTGTCCGCGG
GAGGGTGGCGCTGCCGGCGGCCCGGCCGCTCCCGCTGCAATTGCTCGCTGGGCTCGTCGTGCCCTGCCAGTGGGGCCCCCGCAGCTCTCGTCCCGGCCGC
CGCTGGTGACCACTCGCCGCCCCTCCGGAGGCTTCACCCGCGCCCTCCCCCAGGACGCGCCAGCGGAGCTCCGGCTCCTTCGCCCTGGACGCGGAGGCCG
CGGTGTGCGGGGCGACGGCGAGGCCGGAAGATGGCCTGGGTGCTCAAGATGGACGAGGTGATCGAGTCCGGGCTGGTGCACGACTTCGACGCCAGCCTCT
CGGGCATCGGGCAGGAACTGGGCGCCGGCGCTTACAGCATGAGTGATGTCTTGGCATTGCCCATTTTCAAGCAGGAAGATTCCAGCCTTCCATTGGATGG
TGAAACAGAGCACCCACCCTTTCAGTATGTGATGTGTGCTGCAACGTCACCAGCAGTAAAACTGCATGATGAAACGCTTACTTATTTGAACCAAGGTCAG
TCATATGAAATTCGGATGCTGGATAATCGGAAAATGGGTGATATGCCTGAGATCAATGGAAAATTAGTAAAGAGCATCATAAGGGTTGTATTCCATGACA
GACGGCTACAATACACAGAGCATCAGCAACTTGAAGGATGGAAGTGGAATCGCCCAGGAGACAGACTTCTTGATTTAGATATTCCAATGTCTGTGGGAAT
AATTGACACAAGGACGAATCCAAGCCAGTTAAATGCGGTTGAATTTCTGTGGGACCCAGCAAAACGCACCTCTGCTTTCATTCAGGTACACTGCATCAGC
ACAGAATTTACTCCACGGAAGCACGGAGGTGAAAAGGGAGTGCCCTTTAGGATCCAGGTTGACACCTTTAAGCAGAATGAAAATGGAGAATACACAGATC
ATCTACACTCAGCTAGCTGCCAAATCAAAGTTTTTAAGCCTAAAGGTGCAGACAGGAAACAAAAAACTGACCGAGAGAAGATGGAGAAGAGAACAGCTCA
TGAAAAAGAAAAGTATCAGCCGTCCTATGATACCACAATCCTCACAGAGATGAGGCTTGAGCCTATAATTGAAGATGCAGTTGAACATGAGCAGAAAAAG
TCCAGCAAGCGGACTTTGCCAGCAGACTACGGTGATTCTCTGGCAAAGCGAGGCAGTTGTTCTCCGTGGCCCGATGCCCCCACAGCCTATGTGAATAACA
GCCCTTCCCCAGCGCCCACTTTCACCTCCCCACAGCAGAGCACTTGCAGTGTCCCAGACAGCAATTCTTCTTCCCCAAATCATCAGGGAGATGGAGCTTC
ACAGACCTCTGGTGAACAAATTCAGCCTTCAGCTACGATCCAGGAAACACAGCAATGGCTGCTCAAAAACAGATTCTCTTCCTACACAAGACTGTTCTCT
AATTTTTCAGGTGCCGACTTATTAAAACTGACAAAGGAGGATTTAGTTCAAATTTGTGGTGCAGCCGATGGAATTCGGCTCTATAATTCACTGAAGTCAA
GGTCGGTTAGACCCCGTTTAACCATCTATGTCTGCCGGGAGCAGCCAAGCAGCACAGTGCTGCAAGGGCAGCAGCAAGCTGCAAGCAGTGCAAGCGAGAA
TGGCAGTGGGGCACCCTATGTTTATCATGCAATCTACTTGGAAGAAATGATTGCCTCAGAAGTTGCTCGAAAACTTGCGCTGGTGTTTAATATCCCTCTC
CACCAAATTAATCAGGTTTACAGACAGGGTCCCACCGGTATTCACATTCTTGTTAGTGATCAGATGGTTCAGAATTTTCAAGATGAGAGTTGTTTTTTAT
TCTCCACAGTAAAAGCTGAAAGTAGTGATGGCATCCACATAATTTTGAAGTGATGTCTTATATAGACTGAACTGTATTCAGTACCAAATAGTCACGCTTA
AAAGTGTGTGAAGACTGAATCCAAGAAGTCTTGGGATTGGATTTTACCATATGAAATGTTTCATATTGAAAACACAAGATGACCTTTCTAATGAGCTGTA
TGAGAGGTGAATCTCCTCACTGTCACTGCCATAGCCAAGCATCCTCATGAGAGTGAGCACATCGGCACAGCATGCATCCAGCTCTGGAGGCCACGGTGCA
GGCATAGCTGCCTGCTGCTCTGGCAGAGGCCAGTAAATACAGTTCCTAGAAGCAGCCTTTGCTGTCTTTTTACACTGTATGCGGTTTGGAAATGAATGTA
GAAACTTACTGTGGGCATTTACCTTTCTGTGCCAGTTTGGCTTTTATTGCCTGAACCTTATGCTGACCTGGAGAGGAGATGGGGGACAGTGCTGTTGTGG
GGCCAGCAGTGAATCTGTATGCGGAGAGTTGTGTTGTGCTGATGTGGCCGTTGGTGGTCAGGTAAGAGGCTCGGCACCTTCTTGGAAGAAATCATGTCTG
AGGGTGTACGTTTGATATGATCATGCCAGATTGGAGAAGATCCAAGCCAGGAAGATGGGCTTGAAGCAAACTGCATTATCAGGAGTACCTTGGTGAGAGG
ATCAGTGTAAATCCTAATAGGTACAAAGACTTTTGTGTTTTGGCTTTGTCACAGATTTATTGAAAAACTTTTTTGCTTCTGCTTCCATTTTTAGCATTTT
AGTTTCTGGTTTTCATTTTTGGAGATTCCTTGCCTTTTAAACTCGTGGTTTTTCTCTCATTTTCTTCCCTCTCTCCCTCCATCTCTGACCACCCCCACCC
TAACCCCCCACCCCCACCATCCTATTAAACATTTTTAAAGCCCTACCCCAGACATTGGAAATAGGTGACCCAAGTAGGGGGAGAAAGTATTATTGTTGAT
AGCTTCTGACTAGGTGTTAAGGGATCTTCATTATGAACAAGATGAATTTTTTTCTGGAAACACTAGATGTTATCAATCAAACACTAAAATGTACCATACA
AATCCCTTAAGCCTCTCAAATATTGAGCTTTAGTACAATCATGGATAGACATTCTGGTGATGATTTAGGGGCTTTTTATACACCACATACTAGCTTCTTT
CTCTATAAGAGTGCCTCTTTCATAAAACCAAATGCTTGTCTGCTAGCATACTTTTCAAAGGGAATCCACTGTTTTCTCACTTTCCTCCCATATCTCCGTC
CTTCATCCAAAACCTTCCCAGAATCCATCAGCAAGCATGTTTGAGGCCTGTGGTGTAGGGGACTGAATTTTTTTTTTAACTTCTATTCCATTTTAATTGT
AGGATATCTTTGTCCATATACCCAGGTGTCCTGATTTGAATGTACTATTTGATCCTCATTGTGTTCAGGCAAAAAATAGGAAATGAGTAATTTTGAGTTT
GAAATCTCTCCCAGAAGACAAACTACTTCAGTGAGTAAAAGCTTTGACATTTTATGTTTTATTCATAAAGGGGGTTAATTATTTGCTACAAAGAAGCACG
ATCTATTTTCATCATCGATTTGAAAATATCTGTAACTCCTATAGATCCTATAGGCAGAGAGTTTTCCTTTCTGACTTTTTCCCTTTGCTTTCGTGTGACC
ACATGTTTTCTGTACCAGTCACTGGGGAAAGAAGTGAGTTTATCTCGTTTGTTTTAAAAGTTTTGCTTGTCTATTTAGCATTCCTTTTTGGGTCTCAAGA
TTTATGGAACAATAAATGTCATTTAATGCTGTGTGCTTATTTTGAATTCCTCATCAGGTTTTAGAAGCGGGGTAAAAATACTTAGATGCTTATCAGACTT
GAAATTATACTGAGTGGCATTGAACGTGAGTTTGTCCCAGTGAAACAGGCTAAATAAATTTTGGCACCAGCAAATTTGTTACTTTGTTTTTTTAATAGTA
GGATGTACACATTTCAGTATAATAAATGTTTTCTGATTGTTTTGCAAA

Loop counts:

3 nts: 1
5 nts: 1
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