Annotated gene sequence

Experiment = in vitro 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

ACGTCGGGTCGGCGGGTGGATGAACGCGGCCCTCTGTAATGGCGGAGCGTGGCGGGGACGGGGGCGAGAGTGAACGATTCAACCCGGGGGAGCTCAGGAT
GGCCCAACAGCAGGCCTTGAGGTTCCGAGGTCCGGCTCCCCCACCAAATGCAGTGATGCGAGGCCCACCACCTCTGATGCGACCTCCTCCACCTTTTGGT
ATGATGCGAGGCCCTCCTCCACCACCACGGCCGCCCTTTGGACGTCCTCCTTTTGATCCTAATATGCCGCCAATGCCTCCTCCAGGAGGGATACCTCCAC
CTATGGGCCCTCCACACCTCCAGAGACCACCTTTCATGCCTCCTCCCATGAGTTCCATGCCTCCTCCTCCGGGTATGATGTTTCCACCAGGAATGCCTCC
TGTGACTGCTCCTGGTACTCCAGCACTACCTCCTACGGAGGAGATATGGGTTGAAAATAAAACTCCAGATGGGAAGGTTTATTATTATAATGCTCGGACA
CGTGAATCTGCATGGACCAAGCCAGATGGAGTTAAGGTTATTCAGCAATCAGAACTGACACCTATGCTTGCAGCCCAGGCACAGGTTCAGGCTCAGGCCC
AGGCGCAGGCTCAGGCCCAGGCGCAGGCTCAGGCCCAGGCACAAGCTCAGGCCCAGGCTCAGGCTCAGGCCCAGGCCCAGGCCCAGGCCCAGGCCCAGGC
CCAAGCCCAAGCCCAGGCCCAGGCTCAGGCTCAGGCACAAGCTCAGGCCCAGGCCCAGGCTCAGGTCCAGGCCCAGGTCCAGGCACAAGTGCAAGCACAA
GCAGTTGGAGCTTCCACCCCTACGACCAGTAGCCCAGCACCTGCAGTATCCACTTCAACATCATCATCCACCCCTTCCTCTACCACTTCTACCACAACAA
CTGCTACTTCAGTTGCGCAGACAGTATCAACACCCACAACACAAGATCAGACCCCAAGTTCTGCTGTTTCAGTTGCCACGCCTACAGTTAGTGTTTCAAC
TCCTGCTCCTACAGCCACACCTGTGCAAACCGTTCCCCAGCCGCACCCTCAGACGTTACCTCCTGCTGTTCCTCATTCAGTACCTCAGCCAACAACAGCA
ATACCTGCTTTTCCACCAGTAATGGTACCTCCGTTTCGTGTTCCCCTTCCTGGCATGCCAATTCCACTTCCAGGTGTAGCAATGATGCAAATAGTCAGCT
GCCCGTATGTAAAGACAGTCGCTACCACCAAGACCGGTGTATTGCCAGGAATGGCCCCTCCTATCGTACCCATGATACATCCCCAGGTTGCTATTGCAGC
TTCACCTGCTACCTTAGCTGGAGCAACAGCAGTTTCTGAATGGACTGAATATAAAACAGCAGATGGGAAGACATATTATTATAATAATAGAACATTAGAA
TCAACCTGGGAAAAACCCCAAGAACTAAAGGAAAAAGAAAAGTTAGAAGAGAAGATTAAAGAGCCAATTAAAGAACCCTCTGAAGAGCCTCTGCCAATGG
AGACGGAGGAGGAGGATCCTAAAGAAGAGCCTATAAAGGAGATAAAGGAGGAGCCCAAAGAAGAGGAGATGACTGAAGAAGAAAAGGCTGCCCAGAAGGC
AAAGCCAGTTGCTACTGCTCCTATTCCTGGTACTCCATGGTGTGTCGTTTGGACTGGTGATGAGCGGGTCTTCTTTTATAATCCCACCACTCGTCTTTCT
ATGTGGGACCGACCTGATGATCTGATTGGCAGGGCAGATGTTGACAAAATTATTCAGGAGCCCCCTCATAAAAAAGGAATGGAGGAATTGAAGAAACTAA
GGCACCCAACTCCGACAATGCTGTCGATCCAAAAGTGGCAATTCTCTATGAGTGCAATTAAAGAGGAACAAGAATTAATGGAAGAAATTAATGAAGATGA
GCCTGTTAAAGCAAAAAAACGGAAGAGAGACGATAATAAAGACATTGACTCAGAGAAAGAAGCTGCCATGGAAGCTGAAATTAAAGCTGCCCGAGAAAGG
GCCATTGTCCCTCTGGAGGCTCGAATGAAGCAGTTCAAGGACATGCTGCTAGAGAGAGGGGTGTCTGCTTTTTCAACGTGGGAGAAGGAGTTGCACAAGA
TAGTTTTTGATCCCCGGTACTTACTTCTCAATCCTAAAGAGAGAAAACAGGTGTTTGATCAGTATGTAAAGACCAGGGCAGAGGAAGAACGCAGGGAAAA
GAAAAATAAAATAATGCAAGCCAAGGAAGATTTCAAAAAAATGATGGAAGAAGCAAAATTTAATCCAAGAGCAACTTTTAGTGAATTTGCAGCCAAGCAT
GCTAAAGATTCAAGATTCAAAGCAATTGAAAAGATGAAAGACCGAGAAGCCTTGTTTAATGAGTTTGTGGCCGCTGCTAGGAAGAAAGAGAAAGAAGATT
CGAAGACCAGAGGTGAGAAGATTAAATCGGATTTCTTTGAACTATTATCTAATCATCACTTGGACAGTCAGTCTCGATGGAGCAAAGTAAAAGACAAAGT
AGAAAGTGATCCACGTTACAAAGCAGTAGATAGTTCATCAATGAGAGAAGACCTTTTCAAACAGTACATTGAAAAAATAGCCAAGAATTTAGACTCAGAA
AAAGAAAAGGAGCTTGAAAGGCAAGCCCGCATTGAGGCAAGCCTTCGAGAACGAGAAAGGGAGGTTCAAAAGGCCCGTTCAGAACAAACAAAAGAAATAG
ATCGAGAGAGAGAGCAGCACAAACGAGAAGAAGCTATCCAGAATTTCAAAGCTCTTCTGTCTGACATGGTACGTTCTTCAGATGTGTCATGGTCTGATAC
TCGTAGGACCCTCCGAAAAGATCACCGCTGGGAATCTGGATCCTTATTGGAAAGAGAGGAGAAAGAGAAGCTTTTTAATGAACACATTGAAGCACTTACC
AAAAAAAAGAGAGAGCACTTTAGGCAACTTCTGGATGAAACTTCTGCAATTACCTTAACATCCACGTGGAAAGAAGTAAAAAAAATCATTAAGGAAGATC
CTCGATGTATTAAGTTCTCCTCCAGTGACAGGAAAAAACAAAGAGAATTTGAAGAATATATCAGAGACAAATATATCACAGCCAAAGCTGACTTCAGGAC
GCTTTTGAAAGAGACCAAATTTATAACATATAGATCCAAAAAATTAATCCAAGAATCAGATCAGCACCTGAAAGATGTAGAAAAAATTTTACAGAATGAC
AAACGGTATCTAGTACTGGACTGTGTGCCAGAGGAGAGGCGTAAACTGATTGTGGCATATGTTGATGACCTGGATCGCCGGGGTCCACCCCCACCTCCCA
CAGCATCGGAGCCCACGAGACGATCAACAAAATAATTCTAAATACTCTTCCATAGGGGCATCTATTCAAAATGCTTGCATGAGCCAATTTTCAGGTTTTT
ACATATATGTGCATTAGTCAACCTATTGCGAAACCATCTGACAAACAGAAGGAGAAGCATTTGTGAACAGTTTCTGAACAGAACACTTTGGAAATATTTA
TGCTTTTCTTTGTGTGGCATGACTGACATACATACTCAAATATAGGCTGTCTCTAGTAAATCTTAAAATCTTGAAGCTAAAATTCATCCTTTTATGAGGT
GTGGAAGTCAGTGACTTGGTGACGTTCTTCCTAGCAGTGTTAATACATGCAAGAAGTAAGAGCATTTGTGGCTTGAACTTGCCAGATGCAAATACCACAG
ACTCCAAGAAAACCCGAGTTGGGGTTTGTTTTGTTTTGATTTTTTTTTTTTAAAGCGGGTAAAAGAGAAAACACTGAAAATTGAATTCTTATCTTCCAGA
GGCTACAATTATTATAATGGACAATACTTTTACCTTTGTCTCTAAAGATCAGATTAGTTTTATTTGTTCACTTACGTGCTTTGATTATCCCCTCTGAATT
ATAGACCGAGTCTTGTTGTTTAGCCTAAGAGAAGATTTATGTAGTAATTTCTTCTCAGGTATGGAACCACGGTCATAACTAACATGTTGGCCAGAATAGA
ACCACTGGTTAAACATATTTTATTCACCATTAAGTGATCTTTATCAATATTCTGGATTAGACAACAAATTACCTTTCTGGGTGTTTCTTGTAAACTATAC
TCCTGTTTGAATGTTAAACTTTGTTGCTAAAGTTTAATTTTAAGATGTTTGAATGTTCAGTTTATGTATTTGAACTACAATAAACCAACCCTTTTTATAT
ATCTGTATTGTATATGATTATTGTTACTTAATTTTTAAGAGCTTATTTTAACCTGTTTTTAAAAGCAGCAAATAGAATTTCCCACAAAGTAAGTTGACTC
TAAATCTTAAGTATTACCTAGTTTTTAAAGGTTTGAATATAATAATGCAGTATTTGCAGTATAAAAAGGAAGGAATTTGTAGAGAATCATTTTGGTGCTC
AAGTCTCTTAGCAGTGCCTTATTGCCTCATAGCAAGAAGATGCTGGGGTTTTTTTTGTTTTTGTCCTTTGTATTAATGTATGATGGTTTGCGCCTTTTTG
GCATTCTTTCAACATGTCGTGTACATCACACCATGAATCAGTTCCTAATTGATATATCTAGCTTTACCTCCCGAGTTAAAAAAAAATCTTTTTATTTTAT
GCCTTCATAGGTTGCTCGTTTCAGAGTGCCACATAAATAAAATGTTTAACAAAA

Loop counts:

3 nts: 1
4 nts: 2
10 nts: 1

Tetra-loop variants:

UUCU    1
UUGC    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: 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