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

CAGCCCGGGATCCCCGGCCTGTCCCTTTAACCCCGCCGCCGGGCGGGAGCACGTGAGCGGGGCTCCGGGTGGCACCCGGGCGCCGCCGCCGCCGAGGCAG
TTGTATTTCGAACGCTGCCTCTGGCTAGCAGCCAGGCGCCTTGGCTCGGCGGTCCGCCTGGCCTCCCTCCTCCTCATACTTTTCTTCCTGCGCAACCCCC
TCCCCTTTATCCGCCCACGATTAGAGGTGGGCACTCCCCCCACCACCACCCCCTCCCCAAGCGCAAGCGCGTGCACGCACACACACCACACACACTCACA
CTCACACACACTCACACACACTCATCCCACTTGAATCTTGGGGCAGGAACTCAGAAAACTTCCAGCCCGGGCAGCGCGCGCTTGGTGCAAGACTCAGGAG
CTAGCAGCCCGTCCCCCTCCGACTCTCCGGTGCCGCCGCTGCCTGCTCCCGCCACCCTAGGAGGCGCGGTGCCACCCACTACTCTGTCCTCTGCCTGTGC
TCCGTGCCCGACCCTATCCCGGCGGAGTCTCCCCATCCTCCTTTGCTTTCCGACTGCCCAAGGCACTTTCAATCTCAATCTCTTCTCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGCAGGGTGGGGGGAAGAGGAGGAGGAATTCTTTCCCCGCCTAACATTTCAAGGGACACAAT
TCACTCCAAGTCTCTTCCCTTTCCAAGCCGCTTCCGAAGTGCTCCCGGTGCCCGCAACTCCTGATCCCAACCCGCGAGAGGAGCCTCTGCGACCTCAAAG
CCTCTCTTCCTTCTCCCTCGCTTCCCTCCTCCTCTTGCTACCTCCACCTCCACCGCCACCTCCACCTCCGGCACCCACCCACCGCCGCCGCCGCCACCGG
CAGCGCCTCCTCCTCTCCTCCTCCTCCTCCCCTCTTCTCTTTTTGGCAGCCGCTGGACGTCCGGTGTTGATGGTGGCAGCGGCGGCAGCCTAAGCAACAG
CAGCCCTCGCAGCCCGCCAGCTCGCGCTCGCCCCGCCGGCGTCCCCAGCCCTATCACCTCATCTCCCGAAAGGTGCTGGGCAGCTCCGGGGCGGTCGAGG
CGAAGCGGCTGCAGCGGCGGTAGCGGCGGCGGGAGGCAGGATGAGCGCACGCGGTGAGGGCGCGGGGCAGCCGTCCACTTCAGCCCAGGGACAACCTGCC
GCCCCAGCGCCTCAGAAGAGAGGACGCGGCCGCCCCAGGAAGCAGCAGCAAGAACCAACCGGTGAGCCCTCTCCTAAGAGACCCAGGGGAAGACCCAAAG
GCAGCAAAAACAAGAGTCCCTCTAAAGCAGCTCAAAAGAAAGCAGAAGCCACTGGAGAAAAACGGCCAAGAGGCAGACCTAGGAAATGGCCACAACAAGT
TGTTCAGAAGAAGCCTGCTCAGGAGGAAACTGAAGAGACATCCTCACAAGAGTCTGCCGAAGAGGACTAGGGGGCGCCAACGTTCGATTTCTACCTCAGC
AGCAGTTGGATCTTTTGAAGGGAGAAGACACTGCAGTGACCACTTATTCTGTATTGCCATGGTCTTTCCACTTTCATCTGGGGTGGGGTGGGGTGGGGTG
GGGGAGGGGGGGGTGGGGTGGGGAGAAATCACATAACCTTAAAAAGGACTATATTAATCACCTTCTTTGTAATCCCTTCACAGTCCCAGGTTTAGTGAAA
AACTGCTGTAAACACAGGGGACACAGCTTAACAATGCAACTTTTAATTACTGTTTTCTTTTTTCTTAACCTACTAATAGTTTGTTGATCTGATAAGCAAG
AGTGGGCGGGTGAGAAAAACCGAATTGGGTTTAGTCAATCACTGCACTGCATGCAAACAAGAAACGTGTCACACTTGTGACGTCGGGCATTCATATAGGA
AGAACGCGGTGTGTAACACTGTGTACACCTCAAATACCACCCCAACCCACTCCCTGTAGTGAATCCTCTGTTTAGAACACCAAAGATAAGGACTAGATAC
TACTTTCTCTTTTTCGTATAATCTTGTAGACACTTACTTGATGATTTTTAACTTTTTATTTCTAAATGAGACGAAATGCTGATGTATCCTTTCATTCAGC
TAACAAACTAGAAAAGGTTATGTTCATTTTTCAAAAAGGGAAGTAAGCAAACAAATATTGCCAACTCTTCTATTTATGGATATCACACATATCAGCAGGA
GTAATAAATTTACTCACAGCACTTGTTTTCAGGACAACACTTCATTTTCAGGAAATCTACTTCCTACAGAGCCAAAATGCCATTTAGCAATAAATAACAC
TTGTCAGCCTCAGAGCATTTAAGGAAACTAGACAAGTAAAATTATCCTCTTTGTAATTTAATGAAAAGGTACAACAGAATAATGCATGATGAACTCACCT
AATTATGAGGTGGGAGGAGCGAAATCTAAATTTCTTTTGCTATAGTTATACATCAATTTAAAAAGCAAAAAAAAAAAAGGGGGGGGCAATCTCTCTCTGT
GTCTTTCTCTCTCTCTCTTCCTCTCCCTCTCTCTTTTCATTGTGTATCAGTTTCCATGAAAGACCTGAATACCACTTACCTCAAATTAAGCATATGTGTT
ACTTCAAGTAATACGTTTTGACATAAGATGGTTGACCAAGGTGCTTTTCTTCGGCTTGAGTTCACCATCTCTTCATTCAAACTGCACTTTTAGCCAGAGA
TGCAATATATCCCCACTACTCAATACTACCTCTGAATGTTACAACGAATTTACAGTCTAGTACTTATTACATGCTGCTATACACAAGCAATGCAAGAAAA
AAACTTACTGGGTAGGTGATTCTAATCATCTGCAGTTCTTTTTGTACACTTAATTACAGTTAAAGAAGCAATCTCCTTACTGTGTTTCAGCATGACTATG
TATTTTTCTATGTTTTTTTAATTAAAAATTTTTAAAATACTTGTTTCAGCTTCTCTGCTAGATTTCTACATTAACTTGAAAATTTTTTAACCAAGTCGCT
CCTAGGTTCTTAAGGATAATTTTCCTCAATCACACTACACATCACACAAGATTTGACTGTAATATTTAAATATTACCCTCCAAGTCTGTACCTCAAATGA
ATTCTTTAAGGAGATGGACTAATTGACTTGCAAAGACCTACCTCCAGACTTCAAAAGGAATGAACTTGTTACTTGCAGCATTCATTTGTTTTTTCAATGT
TTGAAATAGTTCAAACTGCAGCTAACCCTAGTCAAAACTATTTTTGTAAAAGACATTTGATAGAAAGGAACACGTTTTTACATACTTTTGCAAAATAAGT
AAATAATAAATAAAATAAAAGCCAACCTTCAAAGAAACTTGAAGCTTTGTAGGTGAGATGCAACAAGCCCTGCTTTTGCATAATGCAATCAAAAATATGT
GTTTTTAAGATTAGTTGAATATAAGAAAATGCTTGACAAATATTTTCATGTATTTTACACAAATGTGATTTTTGTAATATGTCTCAACCAGATTTATTTT
AAACGCTTCTTATGTAGAGTTTTTATGCCTTTCTCTCCTAGTGAGTGTGCTGACTTTTTAACATGGTATTATCAACTGGGCCAGGAGGTAGTTTCTCATG
ACGGCTTTTGTCAGTATGGCTTTTAGTACTGAAGCCAAATGAAACTCAAAACCATCTCTCTTCCAGCTGCTTCAGGGAGGTAGTTTCAAAGGCCACATAC
CTCTCTGAGACTGGCAGATCGCTCACTGTTGTGAATCACCAAAGGAGCTATGGAGAGAATTAAAACTCAACATTACTGTTAACTGTGCGTTAAATAAGCA
AATAAACAGTGGCTCATAAAAATAAAAGTCGCATTCCATATCTTTGGATGGGCCTTTTAGAAACCTCATTGGCCAGCTCATAAAATGGAAGCAATTGCTC
ATGTTGGCCAAACATGGTGCACCGAGTGATTTCCATCTCTGGTAAAGTTACACTTTTATTTCCTGTATGTTGTACAATCAAAACACACTACTACCTCTTA
AGTCCCAGTATACCTCATTTTTCATACTGAAAAAAAAAGCTTGTGGCCAATGGAACAGTAAGAACATCATAAAATTTTTATATATATAGTTTATTTTTGT
GGGAGATAAATTTTATAGGACTGTTCTTTGCTGTTGTTGGTCGCAGCTACATAAGACTGGACATTTAACTTTTCTACCATTTCTGCAAGTTAGGTATGTT
TGCAGGAGAAAAGTATCAAGACGTTTAACTGCAGTTGACTTTCTCCCTGTTCCTTTGAGTGTCTTCTAACTTTATTCTTTGTTCTTTATGTAGAATTGCT
GTCTATGATTGTACTTTGAATCGCTTGCTTGTTGAAAATATTTCTCTAGTGTATTATCACTGTCTGTTCTGCACAATAAACATAACAGCCTCTGTGATCC
CCATGTGTTTTGATTCCTGCTCTTTGTTACAGTTCCATTAAATGAGTAATAAAGTTTGGTCAAAACAGATCAA

Loop counts:

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

Tetra-loop variants:

UCUA    1
UUAA    1
AUAG    1
ACUU    1
ACAC    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 3
U x 0 bulge: 0
C x 0 bulge: 1

1 x 1 internal loop variants:

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