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

GCCGCCTGTGTCATCCGCCATTTTGTGAGAAGCAAGGTGGCCTCCACGTTTCCTGAGCGTCTTCTTCGCTTTTGCCTCGACCGCCCCTTGACCACAGACA
TGTCTCGGGATCGGTTCCGGAGTCGTGGCGGTGGCGGTGGTGGCTTCCACAGGCGTGGAGGAGGCGGCGGCCGCGGCGGCCTCCACGACTTCCGTTCTCC
GCCGCCCGGCATGGGCCTCAATCAGAATCGCGGCCCCATGGGTCCTGGCCCGGGCCAGAGCGGCCCTAAGCCTCCGATCCCGCCACCGCCTCCACACCAA
CAGCAGCAACAGCCACCACCGCAGCAGCCACCGCCGCAGCAGCCGCCACCGCATCAGCCGCCGCCGCATCCACAGCCGCATCAGCAGCAGCAGCCGCCGC
CACCGCCGCAGGACTCTTCCAAGCCCGTCGTTGCTCAGGGACCCGGCCCCGCTCCCGGAGTAGGCAGCGCACCACCAGCCTCCAGCTCGGCCCCGCCCGC
CACTCCACCAACCTCGGGGGCCCCGCCAGGGTCCGGGCCAGGCCCGACTCCGACCCCGCCGCCTGCAGTCACCTCGGCCCCTCCCGGGGCGCCGCCACCC
ACCCCGCCAAGCAGCGGGGTCCCTACCACACCTCCTCAGGCCGGAGGCCCGCCGCCTCCGCCCGCGGCAGTCCCGGGCCCGGGTCCAGGGCCTAAGCAGG
GCCCAGGTCCGGGTGGTCCCAAAGGCGGCAAAATGCCTGGCGGGCCGAAGCCAGGTGGCGGCCCGGGCCTAAGTACGCCTGGCGGCCACCCCAAGCCGCC
GCATCGAGGCGGCGGGGAGCCCCGCGGGGGCCGCCAGCACCACCCGCCCTACCACCAGCAGCATCACCAGGGGCCCCCGCCCGGCGGGCCCGGCGGCCGC
AGCGAGGAGAAGATCTCGGACTCGGAGGGGTTTAAAGCCAATTTGTCTCTCTTGAGGAGGCCTGGAGAGAAAACTTACACACAGCGATGTCGGTTGTTTG
TTGGGAATCTACCTGCTGATATCACGGAGGATGAATTCAAAAGACTATTTGCTAAATATGGAGAACCAGGAGAAGTTTTTATCAACAAAGGCAAAGGATT
CGGATTTATTAAGCTTGAATCTAGAGCTTTGGCTGAAATTGCCAAAGCCGAACTGGATGATACACCCATGAGAGGTAGACAGCTTCGAGTTCGCTTTGCC
ACACATGCTGCTGCCCTTTCTGTTCGTAATCTTTCACCTTATGTTTCCAATGAACTGTTGGAAGAAGCCTTTAGCCAATTTGGTCCTATTGAAAGGGCTG
TTGTAATAGTGGATGATCGTGGAAGATCTACAGGGAAAGGCATTGTTGAATTTGCTTCTAAGCCAGCAGCAAGAAAGGCATTTGAACGATGCAGTGAAGG
TGTTTTCTTACTGACGACAACTCCTCGTCCAGTCATTGTGGAACCACTTGAACAACTAGATGATGAAGATGGTCTTCCTGAAAAACTTGCCCAGAAGAAT
CCAATGTATCAAAAGGAGAGAGAAACCCCTCCTCGTTTTGCCCAGCATGGCACGTTTGAGTACGAATATTCTCAGCGATGGAAGTCTTTGGATGAAATGG
AAAAACAGCAAAGGGAACAAGTTGAAAAAAACATGAAAGATGCAAAAGACAAATTGGAAAGTGAAATGGAAGATGCCTATCATGAACATCAGGCAAATCT
TTTGCGCCAAGATCTGATGAGACGACAGGAAGAATTAAGACGCATGGAAGAACTTCACAATCAAGAAATGCAGAAACGTAAAGAAATGCAATTGAGGCAA
GAGGAGGAACGACGTAGAAGAGAGGAAGAGATGATGATTCGTCAACGTGAGATGGAAGAACAAATGAGGCGCCAAAGAGAGGAAAGTTACAGCCGAATGG
GCTACATGGATCCACGGGAAAGAGACATGCGAATGGGTGGCGGAGGAGCAATGAACATGGGAGATCCCTATGGTTCAGGAGGCCAGAAATTTCCACCTCT
AGGAGGTGGTGGTGGCATAGGTTATGAAGCTAATCCTGGCGTTCCACCAGCAACCATGAGTGGTTCCATGATGGGAAGTGACATGCGTACTGAGCGCTTT
GGGCAGGGAGGTGCGGGGCCTGTGGGTGGACAGGGTCCTAGAGGAATGGGGCCTGGAACTCCAGCAGGATATGGTAGAGGGAGAGAAGAGTACGAAGGCC
CAAACAAAAAACCCCGATTTTAGATGTGATATTTAGGCTTTCATTCCAGTTTGTTTTGTTTTTTTGTTTAGATACCAATCTTTTAAATTCTTGCATTTTA
GTAAGAAAGCTATCTTTTTATGGATGTTAGCAGTTTATTGACCTAATATTTGTAAATGGTCTGTTTGGGCAGGTAAAATTATGTAATGCAGTGTTTGGAA
CAGGAGAATTTTTTTTTCCTTTTTATTTCTTTATTTTTTCTTTTTTACTGTATAATGTCCCTCAAGTTTATGGCAGTGTACCTTGTGCCACTGAATTTCC
AAAGTGTACCAATTTTTTTTTTTTTACTGTGCTTCAAATAAATAGAAAAATAGTTATAATATTGATCTTCAACTTTGCCATTCATGCTTCTATGCATATT
AGGCTACGTATTCCACATTGAAAGCATGAGAGTGTCTAGGCCTTTGAATGGCATATGCCATTTCTGGGAAATGCATCTGGAGGCTAAGTATTGCTTTCTA
CAAATAATTGCCCCCTTTGTTTTAAAAAGAAGAAATGCATATTGAAGTAGTTTGATGATTTGTTTGGCATATAGGAAGCACGCTGGTGCTAAGTATTTTT
TAAATGGTTATGTAAGCAAAGCTGAACTGTAAATCTTCAGGAATATGTATTAAGATTGTGGAATGGGTGTAAGACAATTGGTAGGGGGTGAAAGTGGGTT
TGATTAAATGGATCTTTTATGGCCCTATGATCTATCCTTTACTTGAAAGCTTTTGAAAAGTGGAAAGGTCATTTTGTTGCATTTCCCCATTTCTTGTTTT
TAAAAGACCAACAAATCTCAAGCCCTATAAATGGCTTGTATTGAACTTTTACATTTGAATTAAAGATGTTAAACATGAAGTCTTTTCATGTATTCAAGTG
ATTTATAAAGATGGGGTGTAGTCTAAAAAACAAAACTTGAAAGTAAGAAGGTTTAGTAACTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACT
TTGGGAGGCTGAGGTGGGCAAATCATGAGATCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCT
GGGCGTGGTGGCAGGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGCCAGGAGAATTGCTTGAACCTGGAGATGGAGGTTGCAGTGAGCTGAGACTGCC
ACTGCACTCCAGCCTGGACAACAGAGCGAGACTCTGTCTCAAAAAAAAAAAAAGGTTTAGTACTGAAGTAGGTTTAGTTATATATACATTTGTACTCTGT
AACTTTTACATCTCCTTGTGCTACTTCTGTTGGGCAAAATCTATAGGACTATAAAAATCTATTGGTTCTCTTCTAAGAGCTAGTGGTGATTGTTAACAAA
TAGGGTTGCAGATAATCATTCTTATTGTAAATTTAACTTGTTTTCACATAGTTTCGTTTTCATGTAGCACTAAATCTGGAGAAAGTTGCTCATGCTACAC
AGTACAAATATCCCTTCCTCCCACCATAAAGGCTTGGAATGTTTCCA

Loop counts:

3 nts: 2
4 nts: 2
5 nts: 5
6 nts: 5
7 nts: 2
8 nts: 3

Tetra-loop variants:

UAUU    1
GCUG    1

Single bulge variants:

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