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

TGCTTACGCGCACGCGCATTCCTTGCTAGGGAGAAAGTGCGTGAGCCCTACCTTGGGGCGCCAGAGGCCGCCACAACGCAGGCGCATTCAGCTAAGGACC
ACTCCCTCCCCCCGCACTCCTGCCTCGCCATTTCCCCTCCCTGGCCGGCCGGCCGGCCTTCTTCGCTTTGCGCACGTACCTTTTGAGGTAACGGCCCAAA
GAGGTAGAAGCGCTTTTCCCGCCCGGCCGCGGGGCGTGGCTCTGCGCGCAGCTTGATGACGACGTTTTGGCGCGGTGGCGGAATGGCGGCTTCCACCTCT
GAAGCGGGCGACGCTATGGGTCCCACAGTGGTTTGCTAAGAAGGCCATTTTCAACTCTCCATTGGAGGCTGCTATGGCGTTCCCTCACCTGCAGCAGCCC
AGCTTTCTACTGGCCAGCCTGAAAGCTGACTCTATAAATAAGCCCTTTGCACAGCAGTGCCAAGACTTGATTAAAGTAATTGAGGATTTTCCAGCAAAGG
AGCTGCACACCATCTTCCCATGGCTGGTAGAGAGCATTTTCGGCAGCCTAGACGGTGTCCTCGTTGGCTGGAACCTCCGCTGCTTACAGGGGCGTGTGAA
TCCTGTGGAGTACAGCATCGTGATGGAATTTCTCGACACTGGTGGCCCAATGATGAAGTTGGTTTATAAGCTTCAAGCTGAAGACTATAAGTTCGACTTT
CCTGTCTCCTACCTGCCTGGTCCTGTGAAGGCGTCCATCCAGGAGTGCATCCTCCCTGACAGTCCTCTGTACCACAACAAGGTCCAGTTCACCCCTACTG
GGGGCCTTGGTCTGAACCTGGCCCTGAATCCATTCGAGTATTACATATTCTTCTTTGCCTTGAGCCTCATCACTCAGAAGCCACTCCCTGTGTCCCTCCA
CGTCCGTACTTCAGACTGTGCCTATTTCATCCTGGTGGACAGGTACCTGTCATGGTTCCTGCCCACCGAAGGCAGTGTGCCCTGCCACTCTCCTCCAGCC
CAGGGGGGACCAGCCCCTCACCGCCTCCCAGGACACCAACCATGCCCTTTGCTTCCTATGGCCTCCACCACACTAGCCTCCTGAAGCGACACATCTCTCA
TCAGACGTCTGTGAATGCAGACCCCGCCTCCCACGAGATCTGGAGGTCAGACACTGCTCCAGGTTTTTGTTGAAATGTGGCTTCATCACTATTCGTTGGA
GATGTATCAAAAAATGCAGTCCCCTCATGCCAAGGAGTCGTTCACGCCTACTGAGGAGCATGTGTTGGTGGTGCGCCTGCTGCTGAAGCACCTGCACGCC
TTTGCCAACAGCCTGAAGCCAGAGCAGGCCTCACCCTCCGCCCACTCCCACGCCACCAGCCCCCTGGAGGAGTTCAAACGGGCCGCTGTCCCGAGGTTCA
TCCAGCAGAAACTCTACCTCTTCTTGGAGCATTGCTTTGGCCACTGGCCCCTGGACGCATCGTTCAGAGCTGTCCTGGAGATGTGGCTGAGCTACCTGCA
GCCGTGGCGGTACGCGCCTGACAAGCAGGCTTCAGGCAGCGACTCCCAGCCCCGGTGTGTGTCGGAGAAATGGGCGCCCTTTGTCCAGGAGAACCTGCTG
ATGTACACCAAGTTGGTTGTGGGCTTCCTGAACCGCGCACTCCGCACAGACCTGGTTAGCCCCAAGCATGCGCTCCTGGTGTTCTGAGTGGCCAAAGTCT
TTGCCCAGCCCAACCTGGCTGAGATGATTCAGAAAGGTGAGCAGCTATTCCTGGAGCCAGAGCTGGTCATCCCCCACCGCCAGCACCGACTCTTCACGGC
CCCCACATTCACTGGGAGCTTCCTGTCACCCTGGCCACCAGCGGTCACTGATGCCTCCTTCAAGGTGAAGAGCCACGTCTACAGCCTGGAGGGCCAGGAC
TGCAAGTACACCCCAATGTTTGGGCCCGAGGCCCGCACCCTGGTCCTGCGCCTCGCTCAGCTCATCACAGAGGCCAAACACACAGCCAAGTCCATCTCCG
ACCAGTGTGCGGAGAGCCCGGCTGGCCACTCCTTCCTCTCATGGCTGGGCTTTAGCTCCATGGACACCAGTGGCTCCTACACAGCCAACGACCTGGACGA
GATGGGGCAAGACAGTGTCCGGAAGACAGATGAATACCTGGAGAAGGCCCTGGAGTACCTGCGCCAGATATTCCGGCTCAGCGAAGCGCAGCTTAGGCAG
TTCACACTCGCCTTGGGCATCACCCAGGATGAGAATGGAAAACAGCAGCTCCCCGACTGCGTCGTGGGTGAGAACGGACTCATCCTTACGCCCCTGGGGC
GGTACCAGTTCGCAGGACAGATGGCGGCTCTGTGTTCCCGGGATGACTTCCTCGGCAGCTTCTGTCGCTACCACCTCACAGAACCTGGGCTGGCCAGCAG
GCACCTGCTGAGTCCTGTGGGGCGGAGGCAGGTGGCCGGCCACACCCGCGGCCCCAGGCTCAGCCTGCGCTTCCTGGGCAGTTACCGGACGCTGGTCTCG
CTGCTGCTGGCCTTCTTCGTGGCCTCTCTGTTCTGCGTCGGGCCCCTCCCATGCATGCTGCTGCTCACCCTGGGCTACGTCCTCTACGCCTCTGCCATGA
TACTGCTGACCGAGCGGGGGAAGCTGCACCAGCCCTGAAGGTGGCAGCTGCCTTCAGAGCAGGCTGGAGGGATTTGCCACACAGCCCCACCCTTGGGCTG
AGAGGACCTGGGAAGCCCCTCCAGGAGGGAACACGGTCATCCTCAGGCTTCTGGAGCGGGGTTCCTGCAGCCGCAGAGGCATCTGGAGGAAACACAACCA
AGAAAGGAAGGCAGTTGGGCCCCAGCAAAGGAGTGGCTACCAGGGCTCAACAGCCACGCTCTGTGACAGCGCAGAGCTCAGCGCCGGCCTTTCCCTCCCT
CTGCCAAGGACTCATGGCCAAGCCAGCTCTCGGGGCCTTTTTTCCAGTGCCCATTTGGCTACTCTGCTGCACCAAGCTTGGGAGCCAGCCTGCCAAGAGC
CGCCTGGGCCTGGCCTCCCCACTGGCTGGCCTTGAGGTAGGCAGAGTGGGTTGTGGCGCCTCCTCTCTCTGTGTGGGACCAGGACGGTGGCTTAAGTCTC
CACTCCAGGAAAGAATCAAAGTTTCTAGAGTTGTGAGAAAACCAGAGAGTGGCTCTCCTGATTCTTCACTCTGGGGTGCGTTCTTCATGTTCTCCCAGCT
GTTCCAAGACTGGGCCGTAGAATTCCATGTTTCAGGAGCCTAAGACCCTCCCAGAGCCCAGGTGCTTCACCGCAGACCGCAAGCCATTGAGCACATCACC
CAAAGCAGTGGCCAACATCGCGGACCCCTGTGCCTTGTCACAGATGGGTGCTGGTCCTCAGGCGTTGGGGACACTGCTGGGTCGATGGGGTCGGATTCTG
CCAGTTTCTGCTCTGCAGCCAAAGATGGTCAGAAGCATTGTCACTTCAGTAACATCAAGTGCTCAAAGACATGGCAACCGTTCAGTGGTACTTAAGTATT
CAAAATATACAACTACAGATTCTCTGACAGAAACCAGCACGGGGTCTTCACCTTCATTCACCCCACAGGCGACATGCGAGGGAGAACAGCATCTCAGTGG
TGATTTCCAAACCAAGCCTTTGTTTTCGGTGTGGGGTTTTGGGGGTTTGCTTTAATGTTTTTGAAATTGTAAATGTTGGGCTTTGTATTTTGATGTAAAC
TGAGAATAATGGCATTTTAGGGCCTGTGACCAAAAATGAAGCTTGTAACGACCATGGATCTGAATAAACATGTCCTTGCTTCTGA

Loop counts:

3 nts: 1
4 nts: 1
9 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