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

GGAAAAAAGCGACTTGTGGCGGTCGAGCGTGGCGCAGGCGAATCCTCGGCACTAAGCAAATATGGACCTCGCGGCGGCAGCGGAGCCGGGCGCCGGCAGC
CAGCACCTGGAGGTCCGCGACGAGGTGGCCGAGAAGTGCCAGAAACTGTTCCTGGACTTCTTGGAGGAGTTTCAGAGCAGCGATGGAGAAATTAAATACT
TGCAATTAGCAGAGGAACTGATTCGTCCTGAGAGAAACACATTGGTTGTGAGTTTTGTGGACCTGGAACAATTTAACCAGCAACTTTCCACCACCATTCA
AGAGGAGTTCTATAGAGTTTACCCTTACCTGTGTCGGGCCTTGAAAACATTCGTCAAAGACCGTAAAGAGATCCCTCTTGCCAAGGATTTTTATGTTGCA
TTCCAAGACCTGCCTACCAGACACAAGATTCGAGAGCTCACCTCATCCAGAATTGGTTTGCTCACTCGCATCAGTGGGCAGGTGGTGCGGACTCACCCAG
TTCACCCAGAGCTTGTGAGCGGAACTTTTCTGTGCTTGGACTGTCAGACAGTGATCAGGGATGTAGAACAGCAGTTCAAATACACACAGCCAAACATCTG
CCGAAATCCAGTTTGTGCCAACAGGAGGAGATTCTTACTGGATACAAATAAATCAAGATTTGTTGATTTTCAAAAGGTTCGTATTCAAGAGACCCAAGCT
GAGCTTCCTCGAGGGAGTATCCCCCGCAGTTTAGAAGTAATTTTAAGGGCTGAAGCTGTGGAATCAGCTCAAGCTGGTGACAAGTGTGACTTTACAGGGA
CACTGATTGTTGTGCCTGACGTCTCCAAGCTTAGCACACCAGGAGCACGTGCAGAAACTAATTCCCGTGTCAGTGGTGTTGATGGATATGAGACAGAAGG
CATTCGAGGACTCCGGGCCCTTGGTGTTAGGGACCTTTCTTATAGGCTGGTCTTTCTTGCCTGCTGTGTTGCGCCAACCAACCCAAGGTTTGGGGGGAAA
GAGCTCAGAGATGAGGAACAGACAGCTGAGAGCATTAAGAACCAAATGACTGTGAAAGAATGGGAGAAAGTGTTTGAGATGAGTCAAGATAAAAATCTAT
ACCACAATCTTTGTACCAGCCTGTTCCCTACTATACATGGCAATGATGAAGTAAAACGGGGTGTCCTGCTGATGCTCTTTGGTGGCGTTCCAAAGACAAC
AGGAGAAGGGACCTCTCTTCGAGGGGACATAAATGTTTGCATTGTTGGTGACCCAAGTACAGCTAAGAGCCAATTTCTCAAGCACGTGGAGGAGTTCAGC
CCCAGAGCTGTCTACACCAGTGGTAAAGCGTCCAGTGCTGCTGGCTTAACAGCAGCTGTTGTGAGAGATGAAGAATCTCATGAGTTTGTCATTGAGGCTG
GAGCTTTGATGTTGGCTGATAATGGTGTGTGTTGTATTGATGAATTTGATAAGATGGACGTGCGGGATCAAGTTGCTATTCATGAAGCTATGGAACAGCA
GACCATATCCATCACTAAAGCAGGAGTGAAGGCTACTCTGAACGCCCGGACGTCCATTTTGGCAGCAGCAAACCCAATCAGTGGACACTATGACAGATCA
AAATCATTGAAACAGAATATAAATTTGTCAGCTCCCATCATGTCCCGATTCGATCTCTTCTTTATCCTTGTGGATGAATGTAATGAGGTTACAGATTATG
CCATTGCCAGGCGCATAGTAGATTTGCATTCAAGAATTGAGGAATCAATTGATCGTGTCTATTCCCTCGATGATATCAGAAGATATCTTCTCTTTGCAAG
ACAGTTTAAACCCAAGATTTCCAAAGAGTCAGAGGACTTCATTGTGGAGCAATATAAACATCTCCGCCAGAGAGATGGTTCTGGAGTGACCAAGTCTTCA
TGGAGGATTACAGTGCGACAGCTTGAGAGCATGATTCGTCTCTCTGAAGCTATGGCTCGGATGCACTGCTGTGATGAGGTCCAACCTAAACATGTGAAGG
AAGCTTTCCGGTTACTGAATAAATCAATCATCCGTGTGGAAACACCTGATGTCAATCTAGATCAAGAGGAAGAGATCCAGATGGAGGTAGATGAGGGTGC
TGGTGGCATCAATGGTCATGCTGACAGCCCTGCTCCTGTGAACGGGATCAATGGCTACAATGAAGACATAAATCAAGAGTCTGCTCCCAAAGCCTCCTTA
AGGCTGGGCTTCTCTGAGTACTGCCGAATCTCTAACCTTATTGTGCTTCACCTCAGAAAGGTGGAAGAAGAAGAGGACGAGTCAGCATTAAAGAGGAGCG
AGCTTGTTAACTGGTACTTGAAGGAAATCGAATCAGAGATAGACTCTGAAGAAGAACTTATAAATAAAAAAAGAATCATAGAGAAAGTTATTCATCGACT
CACACACTATGATCATGTTCTAATTGAGCTCACCCAGGCTGGATTGAAAGGCTCCACAGAGGGAAGTGAGAGCTATGAAGAAGATCCCTACTTGGTAGTT
AACCCTAACTACTTGCTCGAAGATTGAGATAGTGAAAGTAACTGACCAGAGCTGAGGAACTGTGGCACAGCACCTCGTGGCCTGGAGCCTGGCTGGAGCT
CTGCTAGGGACAGAAGTGTTTCTGGAAGTGATGCTTCCAGGATTTGTTTTCAGAAACAAGAATTGAGTTGATGGTCCTATGTGTCACATTCATCACAGGT
TTCATACCAACACAGGCTTCAGCACTTCCTTTGGTGTGTTTCCTGTCCCAGTGAAGTTGGAACCAAATAATGTGTAGTCTCTATAACCAATACCTTTGTT
TTCATGTGTAAGAAAAGGCCCATTACTTTTAAGGTATGTGCTGTCCTATTGAGCAAATAACTTTTTTTCAATTGCCAGCTACTGCTTTTATTCATCAAAA
TAAAATAACTTGTTCTGAAGTTGTCTATTGGATTTCTTTCTACTGTACCCTGATTATTACTTCCATCTACTTCTGAATGTGAGACTTTCCCTTTTTGCTT
AACCTGGAGTGAAGAGGTAGAACTGTGGTATTATGGATGAGGTTTCTATGAGAAGGAGTCATTAGAGAACTCATATGAAAGCTAGAGGCCTTAGAGATGA
CTTTCCAAGGTTAATTCCAGTTGTTTTTTTTTTTTTTTAAGTTTATAAAAGTTTATTATACTTTTTTAAAATTACTCTTTAGTAATTTATTTTACTTCTG
TGTCCTAAGGGTAATTTCTCAGGATTGTTTTCAAATTGCTTTTTTAGGGGAAATAGGTCATTTGCTATATTACAAGCAATCCCCAAATTTTATGGTCTTC
CAGGAAAAGTTATTACCGTTTATGATACTAACAGTTCCTGAGACTTAGCTATGATCAGTATGTTCATGAGGTGGAGCAGTTCCTGTGTTGCAGCTTTTAA
CAACAGATGGCATTCATTAAATCACAAAGTATGTTAAAGGTCACAAAAGCAAAATAACTGTCTGAGGCTAAGGCCCACGTGGGACAGTCTAATACCCATG
AGTACTCAACTTGCCTTGATGTCTGAGCTTTCCAGTGCAATGTGAATTTGAGCAGCCAGAAATCTATTAGTAGAAAGCAAGACAGATTAATATAGGTTAA
AACAATGATTTAAATATGTTTCTCCCAATAATTATCTCTTTCCCTGGAATCAACTTGTATGAAACCTTGTCAAAATGTACTCCACAAGTATGTACAATTA
AGTATTTTAAAAATAAATGGCAAACATTAAAAACAA

Loop counts:

3 nts: 10
4 nts: 8
5 nts: 4
6 nts: 1
7 nts: 3
8 nts: 2
9 nts: 1
10 nts: 1

Tetra-loop variants:

GAGA    1
GGAA    1
AGAA    1
UGAA    1
ACCC    1
AGCA    1
UCAA    1
UUAC    1

Single bulge variants:

G x 0 bulge: 0
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: 1
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