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

CTAGTTAAGGCGGCACAGGGCCGAGGCGTAGTGTGGGTGACTCCTCCGTTCCTTGGGTCCCGTCGTCTGTGATACTGCAGCGCAGCCATGGCAGAACCGC
AGCCCCCGTCCGGCGGCCTCACGGACGAGGCCGCCCTCAGTTGCTGCTCCGACGCGGACCCCAGTACCAAGGATTTTCTATTGCAGCAGACCATGCTACG
AGTGAAGGATCCTAAGAAGTCACTGGATTTTTATACTAGAGTTCTTGGAATGACGCTAATCCAAAAATGTGATTTTCCCATTATGAAGTTTTCACTCTAC
TTCTTGGCTTATGAGGATAAAAATGACATCCCTAAAGAAAAAGATGAAAAAATAGCCTGGGCGCTCTCCAGAAAAGCTACACTTGAGCTGACACACAATT
GGGGCACTGAAGATGATGAGACCCAGAGTTACCACAATGGCAATTCAGACCCTCGAGGATTCGGTCATATTGGAATTGCTGTTCCTGATGTATACAGTGC
TTGTAAAAGGTTTGAAGAACTGGGAGTCAAATTTGTGAAGAAACCTGATGATGGTAAAATGAAAGGCCTGGCATTTATTCAAGATCCTGATGGCTACTGG
ATTGAAATTTTGAATCCTAACAAAATGGCAACCTTAATGTAGTGCTGTGAGAATTCTCCTTTGAGATTTCAGAAGAAAGGAAACAATGTGATTCAAGATA
TTTACATACCAGAAGCATCTAGGACTGATGGATCACTGTCCCGATTCAAATTATTCTTCAGTCCATTTCCCCTTCCTATTTCAGCTGTTCCTTTTCACCT
AACTGTTCAGTCATTCTGGTTTTCAAGCAGTGCTTTATCTCATGTCCTTGAATATAGTTGTGTAACTTTATTTTTTAGGTAATAATTAGAACAGTTCCCT
TCAGAGGCTGCATTTGCCTTCTTCTGCCACCTAAATATTACTTCCCTTCAAATCTGCCTTTGAATCATCATTTTTAAAAAAAAATTAACATGTTTTTGTT
GTAGTTATCTTCTGGGGTTTCAATTCCTCAGAAACAACTTTTTTCACAACGGAAAGGAAAGAACACTAGTGTTCTTTCAGTAAAGTACAAAGTGTTTATT
TTACAAAAGAGTAGGTACTCTTGAGAGCAATTCAAATCATGCTGACAAGGATACTGATAGAAAAAGTGATTTCTTCTTATTATAAAGTACATTTAAAGTT
CAAGGACTAACCTTATTTATTTGGGAAAGGGGAGGAGGAAGGAAATGATATGGTACCCAGACACTGGGCTAGGCTGCAACTTTATCTCATTTAATACTCC
CAGCTGTCATGTGAGAAAGAAAGCAGGCTAGGCATGTGAAATCACTTTCATGGATTATTAATGGATTTAAGAGGGCATCAATCAGCTCAACTCAAGATTT
CATAATCATTTTTAGTATTTAGATTGTGCCTCAAAGTTGTAGTACCTCACAATACCTCCACTGGTTTCCTGTTGTAAAAACCTTCAGTGAGTTTGACCAT
TGTGCTCTTGGCTCTTGGGCTGGAGTACCGTGGTGAGGGAGTAAACACTAGAAGTCTTTAGTACAAAACTGCTCTAGGGACACCTGGTGATTCCTACACA
AGTGATGTTTATATTTCTCATAAAGAGTCTTCCCTATCCCAAGGTCTTCATGATGCCAGTAGCCATATATGATAAATTATGTTCAGTGATAACTTAGTTA
TCAGAAATCAGCTCAGTGGTCTTCCCCGCCATGATTCACATTTGATGAGTTTTTAAAAATCAAAGTGATTTTGAAAATCTCTAATGGCTCAGAAAATAAA
AACATCCAGTTTGTGGATGACTATATTTAGATTTCTCTAGACTCTAGTGGAAGACCTTTGGAAAGGCCATGCCAACCGTGCTTGTACTGCTAGAAGCACT
TTATGTTTCCTTTTTGGGTGAAATGGATTTATGTGAGTGCTTTAAACAAATAGCAATACTTATAGACTGAAATAAAATGAAACTTCAAATAAGACTATGT
TTAATTTGTAAA

Loop counts:

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

Tetra-loop variants:

CUAG    1
CUUG    1
AAAC    1
UUUC    1
CUUU    1

Single bulge variants:

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