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

AGTATTGCCTGCACAAATATCTACCAGGTCTGCGACGAATAGCTCCAGCAACTTCGCACCGTGTTTTCCACTCAGCCTACCGACAGGCACTGTGCAGATT
CAAGCGGAGAGATGTCCAAGCAGTGAGGCCGCTGCTGCACCGGCCATCCTGAGCCCCTACTCGGCCTTCCCGTCTCCGCTTCCCCGCCCCGCACTAGGAC
CCCTGCAGATGATCAGGCGGCAGCCGGGGTGATTTCCTTCCTCTTTTGGCAACATGGCGGGCGGAGAAGCTGGAGTGACTCTAGGGCAGCCGCATCTTTC
GCGTCAGGATCTCACCACCTTGGATGTTACCAAGTTGACGCCACTTTCACACGAAGTTATCAGCAGACAAGCCACAATTAACATAGGTACAATTGGTCAT
GTAGCTCATGGGAAATCCACAGTCGTCAAAGCTATTTCTGGAGTTCATACTGTCAGGTTCAAAAATGAACTAGAAAGAAATATTACAATCAAGCTTGGAT
ATGCTAATGCTAAGATTTATAAGCTTGATGACCCAAGTTGCCCTCGGCCAGAATGTTATAGATCTTGTGGGAGCAGTACACCTGACGAGTTTCCTACGGA
CATTCCAGGGACCAAAGGGAACTTCAAATTAGTCAGACATGTTTCCTTTGTTGACTGTCCTGGCCACGATATTTTGATGGCTACTATGCTGAACGGTGCA
GCAGTGATGGATGCAGCTCTTCTGTTGATAGCTGGTAATGAATCTTGCCCTCAGCCTCAGACATCGGAACACCTGGCTGCTATAGAGATCATGAAACTGA
AGCATATTTTGATTCTACAAAATAAAATTGATTTGGTAAAAGAAAGTCAGGCTAAAGAACAATACGAGCAGATCCTTGCATTTGTCCAAGGTACAGTAGC
AGAGGGAGCTCCCATTATTCCAATTTCAGCTCAGCTGAAATACAATATTGAAGTTGTTTGTGAGTACATAGTAAAGAAAATTCCAGTACCCCCAAGAGAC
TTTACTTCAGAGCCCCGGCTTATTGTTATTAGATCTTTTGATGTCAACAAACCTGGCTGTGAAGTTGATGACCTTAAGGGAGGTGTAGCTGGTGGTAGTA
TCCTAAAAGGAGTATTAAAGGTGGGCCAGGAGATAGAAGTAAGACCTGGTATTGTTTCCAAAGATAGTGAAGGAAAACTCATGTGTAAACCAATCTTTTC
CAAAATTGTATCACTTTTTGCGGAGCATAATGATCTGCAATATGCTGCTCCAGGCGGTCTTATTGGAGTTGGAACAAAAATTGACCCCACTTTGTGCCGG
GCTGACAGAATGGTGGGGCAAGTACTTGGTGCAGTCGGAGCTTTACCTGAGATATTCACAGAATTGGAAATTTCCTATTTCCTGCTTAGACGGCTTCTAG
GTGTACGCACTGAAGGAGACAAGAAAGCAGCAAAGGTTCAAAAGCTGTCTAAGAATGAAGTGCTCATGGTGAACATAGGATCCCTGTCAACAGGAGGGAG
AGTTAGTGCTGTCAAGGCCGATTTGGGTAAAATTGTTTTGACCAATCCAGTGTGCACAGAGGTAGGAGAAAAAATTGCCCTTAGCCGAAGAGTTGAAAAA
CACTGGCGTTTAATTGGTTGGGGTCAGATAAGAAGAGGAGTGACAATCAAGCCAACAGTAGATGATGACTGAAGAATACCAGTTAAATAATACATTCGGA
TGGATTTGGAAGTTGGAATTCCTCTTAACAACCAAGGGGTTTATTTTCAAAGCAATATTGGGGAATTGATTTCACAGTTCGTTACCTTAGTAGGTAACGG
TAAGGTTATTCTCTTTTTTTTTTTTTTTTTTTTTGGTTATGAAAACTTAGGGACTAAAATTAATATAAAAATTGGCATAATGTTGGATTGAATCTACATT
TTGGCAGAAGTTAAACATTCCCACATAATGTCAAAATTATACATCATGCAGTTCTGTTTTTTTGTTTGTTTTATTTTGTTTTGTTTTTGAGTCTGGCTCT
GTCACCCAGGCTGGAGTGCAGTGGCGTGATCTGCAACCTCTGCCCCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGAGATTACAGGT
GCGCGCCACCACACTTGGCTAATTTTTGTATTATTAGTAGAGACGGGGTTTCAGCATGTTGGCTAGGCCGGTCTCTCCTGACCTCAGGGTGATCAGCCCA
CCTCGGCCTCACAAAGTGCTGGGATTACAGGCGTGAGCCACCTTGCCCAGCCCACATCATACAGTTTGAAATGAAACTTTGCCACAACCAGCCTTTGCTG
TAGCACACACATATATCACTGAACCTGTTTGAAATAAAGTTTTTTTTCTTTTTCATGATTCGTCTTTGAGTACCTCCAGGCTGAAAGACTGTTGTACCAG
TAAAAACTTAAAGGCACAAATTCTCCTTGAAGACCTTCTCCCTTTTATGTGGCCCCATATTTTATGTTGCTTTATCTTTGAAATTTTGCATGAAAAGGAA
ATGAATGGATTCGAATGAAATTGTCCTTTAGAGCATGATTACTTGTTCCCATGGACAAATATTTTTCTCCCCTTGCTCTTCCTGGCCTGAAACACGGGAA
ACCAGAGTCAAAAGTTATCTCCCTCTCCCTGTGATGCCTTGAGATTTTTTTCTGCGTTGTTTAATGCCTGAAATCCAAGTCTTCCTCCATGGGAAAATAC
TGTTATACCAAATAATTCTAGATGAGTAACAAAGATCTTTTTAGGCCTTCATTTTATGTTTTTTCTTAACTGTTATATTATGATTGTGACATAGATTATA
CTACTACTAATTTTTGGATGTTTCAAAAGGTCAAGAAGTAAAAGATGTTAGAAAGCAA

Loop counts:

3 nts: 5
4 nts: 11
5 nts: 1
6 nts: 1
8 nts: 2
10 nts: 1

Tetra-loop variants:

CCAU    2
UACG    1
GAAA    1
AAAA    1
UAGU    1
GUUU    1
AUUC    1
UAUU    1
GAAG    1
GUAA    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 2
U x 0 bulge: 1
C x 0 bulge: 1

1 x 1 internal loop variants:

G x G bulge: 1
G x A bulge: 1
G x U bulge: 0
G x C bulge: 0
A x G bulge: 1
A x A bulge: 2
A x U bulge: 0
A x C bulge: 2
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: 2
C x U bulge: 0
C x C bulge: 0