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

ACCTGCGCGCGACGCGCGGAAGGAGTTCGCGCGACGACCGCGGGGTCGGCGGGCGGGGCGAGGCCCTGGACGGCGGCGGCAGTGGGGCTCCTCCTTCTGT
TTCCCAGACCGAGAGCCGCGCCGGCACCATGTCAGCTTACCCTAAAAGCTACAATCCGTTCGACGACGACGGGGAGGACGAAGGCGCCCGGCCGGCCCCT
TGGAGGGACGCCCGAGACCTCCCCGACGGGCCCGACGCGCCCGCGGACAGGCAGCAGTACTTGCGGCAGGAGGTCCTCCGCAGGGCTGAGGCCACGGCCG
CCAGCACCAGCAGGTCCCTGGCCCTCATGTACGAGTCCGAGAAGGTTGGGGTCGCCTCTTCCGAGGAGCTCGCCCGTCAGCGAGGAGTCCTGGAGCGCAC
AGAGAAGATGGTGGACAAGATGGACCAAGATTTGAAGATCAGCCAGAAACACATCAATAGCATTAAGAGCGTGTTTGGGGGGCTGGTCAATTACTTCAAA
TCCAAACCAGTAGAGACCCCACCTGAACAGAATGGCACCCTCACCTCCCAGCCCAACAACAGATTGAAAGAAGCTATAAGTACAAGTAAAGAACAGGAAG
CAAAGTACCAGGCCAGCCACCCAAACCTTAGAAAGCTGGATGATACAGACCCTGTCCCCAGAGGGGCTGGTTCTGCCATGAGTACTGATGCTTACCCAAA
GAACCCACACCTTCGAGCCTATCACCAGAAGATCGACAGCAACCTAGATGAGCTGTCCATGGGACTGGGTCGTCTGAAGGACATAGCCCTGGGGATGCAG
ACAGAAATTGAGGAGCAAGATGACATTCTTGACCGGCTGACAACCAAAGTGGACAAGTTAGATGTCAACATAAAAAGCACAGAAAGAAAAGTTCGACAAC
TCTGAAGACAGACGGATTTCCACTCTATTGTGATGAAAAGATTTGAAAGATCTTTTTTTGAACTTCCAAGAAATTTCATTTACTATTTTAGTATGTAAAT
TAATGTGTGTTTGCAAATGTTATAATAGAGTAGGTCTTAAGACATTTTTGCTGTTATAAGGAAGTGTTTGTCCCACATTTTCCTAGGGTTAACACCTCAC
CAAGTTCTTCCAGCAAAATGCTTATTAGAGTTTTTGTCTGAGCACAGTAGCCTGGCCCTGCATATCTTGGGCGTTTGATTACCATGCTGGAATAAGAAGA
GTTGCATTTCTCATTTTAATGAGCATATGGAAAGATGGGAACAGAATTTCAGTCTTGCAGCCATGAGCCTCTATTTCTCATTCCTAAGCCTTACCATGAG
TCAGAGTGTTAAGGGGGCCTGTGAACCAGTCGTTTGGTGGAGGAGGGTCCTTCCCACACCTTTGTTTAGGAGTCATCATTCACACACACACACACACACA
CACACACACACACACACACACACACTCTCTGAGCACATTATCTGTGATTCTTTCATCCTCCCAGAAAGGATCAGTGTTAGAATGGGAAATAGAGTGTGCC
ATCTTGCTCTTTTGTTGGCAGATGTCCCCGCTTCCCTCCAGCCCCCCATCCTTGGCATGTATATTAGTAGGAGGGCTTCACACCAGCACTGCTCACTGCG
ACTCCTGGAAATGTGTGGGGAATTGGGTGAGCCCCTCTTCCCCACGTGCTCCCATCTGTAACTCTCCATCTGTGATTTGCAACAGGTCTTCCACTGGCTC
GAGGCTGCGAGGCTGACCGACAGGGGCGCCCAATAGAGTTTGTGGGAATGGAGTATTGCACAGATGCAGCTGCACAATGGTCTTCCTCCACCCCTCTGGG
AATCACCATTAGGCAGGCCTCAGTAGGGCAAAATGTTTATTTGGTACCGGGGGTCTCCTGACCTGTCTAGCATTCCCACCCACTCTTCTGCACTTCTTGC
AAGGTAACTTGAATCATCACTTATTTCTCTGCCACCTGGTTTTAGGACTGGCACTCTATAAATGACGCTGACTTTGTATAGAAGGATTTTGCTAAGGGGG
CAAAAAGCCCAGATACCATTTTAACTGGCCCAGTTCATTTTCTCCTTTCATTTTACAAAAGAAATCATGCAGAAGCATCAATTAAAACTGATTTATTTAT
GTTGGTACATCCAACAAAATAGTTGGAGCCACAAGGCCCTTGTCTTTTTAAAAAAACAAAATATTTTGAAGATGGTGAAAGTGACTGATTTTAATAATGA
GATAGGTCACTTAAAATAACAGTGCCTTTGACCTTAAAACATGGCACTGGCCCATGTGACCTTTGCCATTTCCCAGTACTTCCCTTTACAGTCTGCAGCC
TATAAACAGTGGTGTCTCAAAGCAAAGGAAACCTCCACAAGTGCTGCAACAGTGCATTAGTTTTTATGTAGCAATTTGTTTATAAAAATTCCCATCCCAT
AATGCATGACCTTCCTAAAAATATCCACAGCCTCCATAGGCAAGGTGAGCTTTCTGTGCTACCCACTTGTTAGATTCCAGCCACCTCAGGGATTCTGATC
CATGTCATTAACGACCATCCCAGGGTGTGAGGGCCTGATTAAAGCTTATCGAACTAGACATTTGTTTATTAGATGAGCTCGGCATTATTATTTTCTCAAT
AACTGGTAGAAGGGAAATTTTAAACATAACACTCAACCCAAACAAAACTACTTCGTGAGGCTTTCAGCAAAAAGGCTGCTTAAAAGCATGAACCCGGGAT
GCAGAGCAGCTTTTGTGCACGGTTCCACTTACTGTAATTGTTTCTGGTTCTTTCCTCTAACACCTTCCATGTATGTCAACTTTTTATCACCGTCAGGCAT
AGACTCGTGGAGATTAGTCATTATAGCTCAGACCTAAGCTAATTATTTAAAATAAATACATGTAAAGGCCACTGCCACATTCTCAGCAGACTTCCACTTG
CCTAATGAGATTAGTGATTCAACTGACTTGAAGCACAGTAACATCTTATTTTATGCACATTCCCTGTCTTTTGCTGGACTGATGAAGCCAGTCACCCGCC
CTTCTCTGTTTTTTGGTTTTTTTTTTCTTAACCCCAGGTATATGGAAGGGGAGTTGCCTTCACTTTTCTGGAAATTTGTCTTCGTCTGACATATTAGAGG
GCCTCGTTTTGTCCTGTTCTTGTTCAGACCCTCTCGTTCTACGTCCTGTGCTGAGGGGACTGTCCGTAAGCTACAGGACAGCGAGCTGGTCCTTTCTGCC
ACTTCTTCCCCACTCCCATGCCCAGGAAGGCCTGGTTGCTGATGCTACTTTATAAATGAGTTGCTTGCATTTTCACAGAGAATGAAGGAAGACGTAACAT
GGCTCCAGAAACTTTTCACATGATGATTGGGATCGACAAAAAAATGCTACCCTCTAGACTAGACACATTTCATGGAGACAAGCAAAATGGTGCCAGGGCT
GGGCTGACTGTGGGATGGGATTTGGTACTGCAGACAGATTTTGATTTCCACAGTTGAGCTGGAAACAAACTGTGCCTTCAAAAAATGACTTTTCTAACTT
AAGGTTGGTTATATGTTAAGTGTGCTACTAACTTAAAAAATAGTGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGTGCTTTGGGAGGCCAAGGCGGG
GGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAACACACAAAAAATTAGCTGGGCGTGGTGGTGGGC
GCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATGGCATGAACCTGGGAGGCAGAGCTTGCAGTGAGCCGAGACAGCGCCATTGCACTCCAGC
CTGGGCAACAGAGCAAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAATAGTGCACTCTCTGGCTGGTCACGGTGGCTCACGCCTGTAATCTCAGCACT
TTGGAAGGCCAAGGCAGGCGGATCACGAGGTCAGAAGATCGAGACCATCCTGGCTAACACAGTGAAACCCCGTCTCTACTAAAAATATAAAAAATTAGTC
GGGCATGGTGGCGGGCGCCTGTAGTCCCAACTACTCGGGAGACTGAGGCAGAAGAATGGCGTGAACTCAGGAGGCGGAGCTTGCAGTGAGCCAAGGCGAC
AGAGCAAGACTCTGTCTCAAAAAATAAAAAATAGTGCACTGTCCTTCGAGAAAGTTTTCTAACATCTAGTAATTTGTAACTTAGAAGTGGAGTTGCCTTG
TGGATGTCTTTTTTGCATTCTGTAGGAAATGAAACGTGAATTTAACTCGGGTTGCAAGAAATAAAAATGTCAGTGCATTTAAATTTC

Loop counts:

3 nts: 1
4 nts: 1
8 nts: 1

Tetra-loop variants:

AAGA    1

Single bulge variants:

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