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

CCACGTCATCGAGCAGCTCCCCCTCCCCTTGCTACAAGTCGCACGCGCGGAAGTAAACACCTCTACGTCATCAGGGCGCGTCCTCGTCTTTCCCCTCCCA
TCTCCTCAGATCGGTGGACGTGCTCGCCTCCACTCGGGGCCAGGTCTATGTCCCGGTTTCCCGCAGTCGCGGGCAGGGCGCCAAGGCGGCAGGAGGAGGG
TGAGCGGTCAAGAGACCTCCAGGAAGAGCGGCTCTCGGCTGTTTGCATCGCCGATAGAGAAGAGAAAGGATGCACGTCCCAGGAGGGAGGAACTACTCCA
ACTTTTCCTATTCAGAAACAAAGAAAAAAGATTATTCAAGCTGTGAGGGACAATTCATTCCTTATTGTTACTGGAAATACAGGAAGTGGTAAAACAACTC
AACTCCCAAAATATCTATATGAAGCAGGGTTTTCACAACATGGTATGATTGGTGTAACTCAACCACGAAAAGTAGCTGCTATATCAGTTGCTCAGAGAGT
AGCTGAAGAAATGAAATGCACTTTGGGATCCAAAGTAGGATACCAAGTTCGTTTTGATGATTGCAGTTCTAAGGAGACAGCAATCAAATATATGACTGAT
GGATGTTTACTGAAACATATTCTGGGAGACCCAAATCTTACCAAATTCAGTGTCATTATTTTGGATGAAGCCCATGAAAGAACTCTAACTACAGATATCT
TATTTGGTTTATTGAAGAAGCTATTTCAGGAGAAGTCTCCTAATAGGAAGGAGCATTTAAAAGTGGTGGTAATGTCAGCAACTATGGAATTAGCCAAGCT
CTCTGCATTCTTTGGAAATTGTCCAATATTTGATATACCTGGAAGGCTTTATCCAGTCAGAGAGAAATTCTGCAATTTGATTGGTCCACGAGACAGAGAA
AATACTGCGTATATTCAAGCGATTGTGAAAGTCACCATGGATATCCATTTGAATGAAATGGCTGGAGACATCTTGGTTTTTCTGACTGGCCAGTTTGAAA
TAGAAAAAAGTTGTGAGTTACTTTTTCAGATGGCAGAGTCTGTTGATTATGATTATGATGTTCAAGATACCACCCTCGATGGCTTGTTAATATTGCCGTG
TTATGGATCAATGACAACAGATCAACAGAGGAGGATATTTTTGCCACCACCACCTGGAATTAGAAAATGTGTCATATCCACCAATATTTCTGCAACGTCT
TTGACAATAGATGGAATCAGATATGTGGTAGATGGTGGCTTCGTGAAGCAGTTAAATCACAACCCCAGATTAGGGTTGGACATCCTGGAGGTGGTTCCAA
TTTCAAAGAGCGAGGCATTACAGCGAAGTGGCCGAGCTGGCAGGACTTCTTCAGGAAAATGCTTTCGGATCTATAGTAAAGATTTTTGGAACCAGTGTAT
GCCTGACCATGTGATCCCTGAAATTAAGAGAACTAGTTTGACATCTGTAGTTCTGACCTTAAAGTGCCTTGCCATACACGATGTCATAAGGTTTCCCTAT
TTGGATCCACCTAATGAGAGACTTATTTTAGAAGCTCTTAAACAACTTTACCAGTGTGATGCTATTGACAGGAGTGGCCATGTCACCAGATTGGGTTTGT
CTATGGTGGAGTTTCCTTTGCCTCCACATCTGACATGTGCAGTAATAAAAGCTGCTTCCCTGGATTGTGAAGATCTACTACTTCCAATAGCAGCAATGTT
GTCTGTGGAAAACGTCTTCATTAGACCTGTTGATCCAGAGTACCAGAAGGAAGCAGAACAGAGACATCGAGAATTGGCAGCTAAAGCTGGAGGATTTAAT
GACTTTGCAACTTTAGCTGTCATCTTTGAACAATGCAAATCAAGTGGAGCTCCAGCTTCATGGTGCCAAAAACACTGGATTCATTGGAGGTGCTTATTTT
CTGCATTTCGTGTGGAAGCTCAACTTCGAGAACTAATCAGGAAGCTTAAACAGCAAAGTGATTTCCCAAAAGAGACCTTTGAAGGCCCTAAACATGAAGT
ACTACGAAGATGTCTTTGTGCGGGCTATTTCAAAAATGTAGCTCGAAGATCTGTTGGGAGAACGTTTTGCACAATGGATGGTCGTGGAAGCCCAGTTCAC
ATTCATCCTTCCTCAGCACTTCATGAACAGGAAACCAAACTTGAATGGATCATTTTTCATGAGGTATTGGTTACCACCAAAGTCTACGCAAGAATTGTAT
GCCCAATCCGTTATGAATGGGTAAGAGACTTGTTACCCAAGTTGCATGAATTTAATGCACATGATTTGAGCAGTGTGGCCCGACGTGAAGTGAGAGAAGA
TGCAAGAAGGAGATGGACAAATAAGGAAAATGTAAAGCAGCTAAAGGATGGAATATCGAAAGACGTCTTAAAGAAAATGCAAAGAAGAAATGATGACAAA
TCCATATCTGATGCACGGGCTCGTTTCCTTGAGAGAAAGCAGCAGAGGACCCAGGACCACAGTGACACACGAAAGGAAACAGGCTAAGGTGGTGAACCCT
CCAATTCAGGAAGTGGGAAAAGGAGCCAGGAAATGTGCTTCTACTTTGCCAGTTATTTCAGACAGCACTACCAAGAGGAGGTGGTCAGCACTTGTTATTG
GCCTATGAACTAAAAGCAAATCAAAGCTCATAAATCAAAGCTCATCAGTTCCCATAAATGCAGTTGTCAAAGAAAAGATTTGGTTGCCATAGTCATAAGC
AATGATACATGAAACCAATGAAAGACAGTACATGTAATAATATTTTCCTCAGTACAATTTTGCTGGCCTTAACTGGTATCAAACGCTGTCATTGAGATGT
TTTCAAAGAACATTGAGTTGTATTTAATCAGCGTGTACTCCATTTGCATTGAAGCATTAAAAATTATTTTTCTTAAAATCTCTTTAAGGCCTTCTTGTTG
CTGTTAGAATAGTGCTATATATCAGGTATGTGACCATTTATTTCAGAAGGCTGAACATAAGAGGTTTCTACTCAGCAATACTTAGATGTCTAACTGTTTA
ATTGCTACAGAGCTTTATAGATATTTAGAGAAAAGACTTAATCAATTAGTAAATAAAATTGCCTATGGCAGGATTCTTTCTTGAATTAATATTAATCCTT
AAATTGATTTTTCTGGGATTATACAAATTCCTTTTTATATAAAAGTATATTGTTTAAAACAGTAGCTATAGCCATTAACCAAAGGACAGATGATATATAT
ATATATGATATATATATATATATAAGTTCTTTTTTAGCTGTACCTACGTACTTATATCAGCACCATGTATGTAGGTGTGATAGTACTTTCAAACAGCGCC
TCCACCTGGCCTACTCTGTTATTTCCACCTGTTTGGGTAGGGCCATTTAACTTCCATTATGCCAAACTTGGGATGGGATTTTCGAAGCAGACAACACTAT
TTCATCGTGTTTCAAATTGGAACCTTGAGGCTAGTTAGTATCACACTCAGGCCACACTCAGCACTTGCCCACTCTTGTTTACTGCCTTGTATTCTAGTTA
TTTGTGTATTTGTCTCCCTCACTAGATTATACGCTCCTTGTGGGCAGGGACTGTGTCTTTTTTCATCTTTGTATCTTTCATGCACCTAGCATAGTGCTTT
GCACATAGTAGTCACTCAGTGTTTGTTAAATAAAGCTATTAGTGTCATTAAAATTCAAAA

Loop counts:

3 nts: 2
4 nts: 1
5 nts: 1
6 nts: 2
10 nts: 1

Tetra-loop variants:

AAGG    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 1
U x 0 bulge: 0
C x 0 bulge: 1

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