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
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: 3
4 nts: 2
6 nts: 2
9 nts: 1
Tetra-loop variants:
AAGA 1
GCUG 1
Single bulge variants:
G x 0 bulge: 1
A x 0 bulge: 0
U x 0 bulge: 1
C x 0 bulge: 1
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