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

GCGCAGCAACCTCCACCAGGCCTCCGCGTCTGGACTCCCGCCCTGCCTCTGGGCCTCCTCCGCCCACCGGCGGCGTCTCCCGCGAAGCCCGCTGGGCCTC
GCTCTCACCCTCCTCCTCCTCCTCACGCCGGGCCTTGCTCTTGGCCTTGGATTTCTGGCTGCGCAGTTCGCGTCCCCGCGGCTCCCCGCCGGCCGCGCGT
TTCCGAGCCATGTTGCTTGTCTGGGCAAATTCCACTTCGCGAGTGACGCACCCGGCCGCGATGCGCTAGAACGCCGGCCCCGCCCCGAGGCGGTGCGCTT
GGCCACGCCCCTTCGTTGGAGGCCTAGTCACGCCCCTAAAGGAAGCTCCACCCCATACCCGTGGCCACTAAAAAACTGCGGGAAGCAGGAAAGAGCACAA
CAGGTTTCTCTCTATTTCCGGTGTATTGTATCCTCACGTTTCCGGAGATTGACGTTGCTCTTGTGTTCTCGCGAGAGGCGGGAAAGGGCGCAGGGTTTGA
AACATGGCGGACGACGTAGACCAGCAACAAACTACCAACACTGTAGAGGAGCCCCTGGATCTTATCAGGCTCAGCCTAGATGAGCGAATTTATGTGAAAA
TGAGAAATGACCGAGAGCTTCGAGGCAGATTACATGCTTATGATCAACATTTAAATATGATCTTGGGAGATGTGGAAGAAACTGTGACTACTATAGAAAT
TGATGAAGAAACATATGAAGAGATATATAAATCAACGAAACGGAATATTCCAATGCTCTTTGTCCGGGGAGATGGCGTTGTCCTGGTTGCCCCTCCACTG
AGAGTTGGCTGAAACAAAGAATTTGTCCTGTATGGAAAACGGGAGACTTTGTACAGTGGCCTCTCTAAAAGTACAAAACATTCATAAGAGAAACCTGCAT
ACATTTTGATATTAAGAAATAATTCCGGGGATTCTTCCACTCCTGAAATGAGTTGATTTGCAGATAACTCACAACTTCTTAAGCTAAATGGTATTTTCAT
TTTTCTCAAGCTCTCCAATAAATATGACCACCAAGATGCAGAACTCTTTCAGGACTTCTTTTGCTCCATTATTCTCACAGATACTTACTGATTTTTCTTT
TCTTTAAATTGGTGTTTCCTTGTAGATTTTTTTAAGTGCGGTCTTCTGTCTTGTGAATTATTTAAAGTAAGCATGTCTTACCTTCACTTAGCACACATTT
GCAGTGCACCTACTGTGTTTGAGGCACCAGGTTTGAGTGCTGGGAACCAGAGTTTTATCAAAATGCTTTCTGGGCCAGACATGGTGGCTCATGCCTGTAA
TCCCAGCACTTTGGGAGGCCAAGGTGGGTGGATCACCTGAGGTCAGGCGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTTTCTCTACTGAAAATAT
AAAAATTAGCCAGGCGTGGTGGCGCATACTTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGTAGACGCTTGAACCCAGGAGGCAGAGGTTGCAGTGAGC
CAAGATCACACCATTGCACTTCAACCTGGTCAACAGAGCGAGACTCCGTGTCAAAAAAAAAAAAAAAAAAGTTTTCTGCCCTCAAGTCTTCTGGGGAGGC
AGATGTTTAAACCAACAATTGCAGGCAGTAAGATTAGTGCTGATAGAATCATGCACATGCAGGATGCCATAGGAGCATGGGGAAGAGCACCCAAATATGG
GAGAAAGGGGCAGAGGGACATTGTAAACATCAACCCTGCAGTAGAAGACAGAGCAAAGCATGATTTCTCTTTTCTCTGGCCTGATTTAATTCTAAGGTCA
GACGTTCAGCTTGATCATAACCTGTTTATAATTATGACTCAGACCATTTTTCCACTCTTGGATCATTGGCCATTAATGATGAGGGGTCTCAAACAACATG
TCTCAGTGACACAGTAAAGCAGAAATTGGCTGAAAGCAAAGCTGTTTTTATTTCTAGCTTCAGTCAGCACATAATGCTTAAAACCTAAAGAGGAAAGTAA
AAGCGTGTTACAATCTCTCAAACTTTATCAAGACAGGGCTTAGAACCTGACATCCTCCGCTATGGTCATTCCATTTTGAAATGTAGAAAATCCAACTTGT
GGATGGTTTGTCTGTAAATGAGCTGAATGTGTGTGCGTGTTCATTATCAAGCACGATATGCTCACAAATGCACAGTACTTTAAGCCTTGTGCAAGAAAGA
TGCTTTCAGTAAACATATTTAAAAGGTTTTATTTTCCTTACTAATGGTACATGCCCCTGCAAGTTCATGGAGAAGAGAAAAACAAGTGTGGGTGAGCTGA
TGGAGGCTTCATCTTAGGTGAGGAGGCAGGAGAGACACCCTCCCTTCACTTGTGCCATCCCCACGCTTTGTCCTTAAGCTGTAGTGGTCCCAGGAGATAA
CCTGTTTACAGCAGCCCATTCAGTATTGAAAAATGAACTCCCTCCTGCAGAATGTTAGAAGAAACAACCTCAAAGACCTCAGGCCGCCTGTGGTCATTAG
TATGTGGCAGCAAGATTGAACCTGCCTGCCTCCTACCTGTGTGAGCCTGTGGTGTGGGTGTGGTACCAAGGCCCTGGCTCTGGGCAGTCTGTTGGCTCCT
GGTGTTCACTAAGGCGTGGGGTGACAGGCCATCTGGCCTCGCTCTGCCAGTCTGCAGTTCTCCCCAGCACTGCATTCATTTTTAGTGGTTTCTGATAGTC
ACACTGAATTCCTGGACACTTTCTTCTCTTCATTCTTAGTTATCTTTCTCCTTTTTCTCCTGGAACTGATAGTTTACACTAAAACTTTTGGCTGTGAGGA
CTTGATTATACACATTTCTAAAACCCATGAACCTTAATATCTGACACTGTTACTCTCATATGCACACACAACTAAAACATACCAACCTACTTCATTTCCT
AGCTGCTAAGATACAAGGGGAGGGACAATAAAAGGTTAACTGCAGAATAGCCACCTATGTGTCAGGAAATGGAGGGAGGGGAGGCAATGTGTGAGTCCTT
TTGGAGCTGGGACTCAATCCACAACAGAGACAGCTCAAGCAGGGCCCTGCCATGGTCCACACTGAGGTTTCCTCTGCAGTGGTGCTGTCCACTGAGGGGT
TATGGTGTGAGGGCCCCTGGGAGCCACGCCTTGGACTTCTGAGTCTGCAGAGCACTCGGCTCCAGCCAGCTGGATGGCAGGTGGTCAGTGGAGCTGGTGA
CTGGTGGTTTCTGCAATGAGGTGTCAGATTAGCCTAAGGGAAGCCTCTTCAGCAAGTATCATGCCTGGATCCCGGTCTTGGTTGTTTTATGAGAGGCCGA
TATGAATTGCCATTGCCTCCCACAAAGAAAAATGGACAAAATATGGGACCACATCTTTGAGATGAAATGTGCCCAAAATGAAAAGTAACTTGAGTATCCC
AAGTTAAACTTAATCATTAGCTGCAAATGGACGATTTTCAAATTTCAAATAGTGATTTTTGAAGATTTGCCCAAACTAGAGTACTATCCCTCTTCACACT
AAGAGGCAGAAAGTGGTTTCACACACCCTTTTATTTAATCAGCTAAAGTGGGTGCGGTGACACACACCTGTAAACTCAACCACTAAGGAGACTGAGGCGG
GAGGATTACTTGAGCCCAGGAGTTCGAGATCAGCCTGAGCAACATAACAAGACCCTGTCTCAAATAATACTTAGCTATTACCCATATTGCTTTTAGCCTG
CTGCCAGGAGGGGAGAAATGTTATTGTTTGAACAGATGTCAGATGTGAGTAATGCTCAGCTGTGTTCAATGTAGAAAATTAATAAAAGTTCCAGGAGTCA
TCCTGGCTAGATCAA

Loop counts:

5 nts: 3
7 nts: 1
10 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