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

AGTCCCGGAACTGCTAGAACGAACCATTCGCATATGGAGGGGGTGACCCACCATCTCAGAACATTAAAAAAGGGAAAGAATCCCCTGGTGAACTACAGTG
AAAGTCTTATTGAGCATTTAAATGGAAATAAAAATATTCAGTGGACCTAATGAAGAGTAGATGACTTTCCCTTCTGTCCCCTCCCCGACAGGCACTCATG
GTACCGGCGCCGGCGCAGCTGTGACTGTCGCTGCAGACGGAAACTGACTGGGGTCAATTCAAGTCATGCAGGCTGTGAGAAACGCGGGGTCGCGGTTCCT
GCGGTCCTGGACTTGGCCCCAGACAGCCGGCAGGGTCGTGGCCAGAACGCCGGCCGGGACCATCTGCACAGGCGCTCGACAGCTCCAAGACGCTGCGGCC
AAGCAGAAAGTTGAACAGAACGCGGCTCCCAGCCACACCAAGTTCAGCATTTACCCTCCCATTCCAGGAGAGGAGAGCTCTCTGAGGTGGGCAGGAAAGA
AATTTGAGGAGATCCCAATTGCACACATTAAAGCATCCCACAACAACACACAGATCCAGGTAGTCTCTGCTAGTAATGAGCCCCTTGCCTTTGCTTCCTG
TGGCACAGAGGGATTTCGGAATGCCAAGAAGGGCACAGGCATCGCAGCACAGACAGCAGGCATAGCCGCAGCGGCGAGAGCTAAACAAAAGGGCGTGATC
CACATCCGAGTTGTGGTGAAAGGCCTGGGGCCAGGACGCTTGTCTGCCATGCACGGACTGATCATGGGCGGCCTGGAAGTGATCTCAATCACAGACAACA
CCCCAATCCCACACAACGGCTGCCGCCCCAGGAAGGCTCGGAAGCTGTGATGGGAAGGAGGCCTGCACTTGGACCTGACCTCAAGCCTCAGCTCCAGTGG
GACCTTGTAAAATGCTCCCTGTCAGAGCTCTCCAGAATATGCTTGTTGGAGATCCTTCAGGCAGTAAGGGAGAGTTTTGCCTCCTTACACAGTGGCCTTT
GCTTGCACCTCCAGCTGGAGATGGGTGTGCCCCAGAAGTAAGCTTTGCATCTCTTACAAGAGGGGAGCTACAGGGGCAGCCGTGGCCTAGGCCCAAACTC
TGCTCTGAGAAAATAAATATCTGTACCACCTGTCATAATTTTGAGATTTTTTGCTTTCAGAGTTACGTAATTCCTAATTCCTCTTGAAAAAGAGAGTGTG
AAATGAGGTGAGGCCTCAGATGAAAGTAAAATATAAATGTGAGTTGCTATTTACCAGACACTTCTGGTTTCAGATATTTCTTTTCTAGCCCCTTACCCAA
GATTTCTAGAGCTAATCCTAGTAACTTTTCTTATTAATGACTTATAATTTGGCCCCAAATTGGAGCTTTTTGCCACCTACCTCTGGATTCTGATGGATTT
CGCCATTATGGGCATGTTTAAAGTTAGCCCTAAACACAGGATTTTCTACAAGTGGACAGTCAAACTCCCCACACTAAAGTGGCAGTCATCGTTTACACTC
CATGGGCTTCAGCAGTCCCAGCACTAACGAGAGAGTGCCCTAAAAGCGGGGAGGGTAGAGTTGTACAAAACATGATTCTTGGCCAGGCACGGTGGCTCAC
ACCTGTAACCCTGGCACTTTGGGAGGCCAAGGCGGGTGGATCACTTGAGTCCAGTTAGAGACCAGCCTGGGCAACATGGTGAAACCCCCTCTCTACTAAA
AATACAAAAATTAACCAGGCATGGTGGTGTGCGCCTGTAATCCCAGCTACTCTGGAGGCTGAGGCATGAAAATCGCTTGAACCCAGGAGGTGGAGGCTGC
AGTGAGCTGAGATCATCCTACTGCACTCCAGCCCAGGTGACAGCGAGACTGTCTCAAAAAAATAAATAAATATAAATAAAAATTTAAAAAAATTAAAAAA
AAAAACCTGATGATTCTCTAGAAAATAGGGTGGATGGCAGGATGGGCTTGAGTAGAGTCCAAATCTAGAAGTGCAGAAAGCAAGTTGATAAGGAACCTGG
GTAGTGCTGGCAGTGGGGCACAACTCAGGACCCCCAGGCAGGACTGACTGCTCCTCTGTTGGGGCTCTAGGGTTCCTGGATACGGCACAGAGGCCAAAGG
TGGGGGCTCTAGAGACACGACCAGAGAGTCCCCTCTTCCACAGGCAAAGACTAAGGGTGAGAGTATCACCAGAAGCTGAGAAGGAGTGGTCAAGTACACA
AAAGCACTGTTCCTCCCAGATGAGTGCAGGAAGGGCTGCTGACCAGAAGGGGAAGGCACTGTGGAGTTTTACTTCTGTGTCCAGCCAGCTAAGTACTGTG
ATCTGCCTGAACTCAGTATAGGAAAAGACACAGATGCCCCCTTAAATAGGCAAGAGGCTGTGTTAGGACAAAGAAAGGAGGAAGATCACGAACCAAGACA
TGAATTTAGAGGAAAAATGCCTCCCTACTGCCTTCTCTTTAGTCCTTAGCAGGTCCTATGAAGGCCATCTTGTGACAGTGACCAAAGAAGCCCAACCGGA
GGCTTCTTGGATCAAAGCCACTGTCGGAAGGAATTAGACTGTTTCACCGCAAAACTACATATAAACACAATGCATTAAAACATGGTGCACTTGAAAATTG
CACTTCGCGATTTGATATGGTTTGGTGGACAGAGGGCCCGTAGCCATCAGACAGTTCAATCAGGGTCTGAGCAGGAAACAGCTCACAAGGTTTAAGAGAA
AAGCTCAATGAAAGCTCTTTGCAGAGGCATGGGTAAGATTAAGGAAATAAAGAAGGTGGACTACAAAGCAGCTGCCACCCTAGGCTAGAAGAGGCAGGGA
AGAACAGTTCCTAGAACCTGGCAGGAGCTGCCACAGCAGCAGAGTGCACCTCTGCCAAAACCATGGCCTGAGGGAGAGGGAAGAAATGCCTGGCTGTTCC
CGGCCTGTAGTCCCTTGCTGGGGTCCCCCTTGGCTGATCCCAAAAGGAAGCAAAAAGGAAGGGAACTCAGTGTTGTGGTACTTGGAGGCTCAGCCTCCCA
GGCTGCAGAGTGGATCTGGAGGGGCACGTAGAGGATAGTAAACACAGGAGGCTTCTGTGGCTTCTGTAAGTCCTCCATACACCATAGGTTTTTATTTTGG
TTTTGGTTTTTGAGTCTCGTTGTCACCCAGGCTGGATTGCAGTGGTACGACCATGGTTCACTGCAGCCTCAAACTCCTGGGCTCAAGTGATCCTCCAGCT
TCAGCCTCCTGTGAGCATCTGGGACTACAGGCGCATGCCACCACACATGGATAATTTTTGTATTTTTTGTATTGAGACCAGGTCTTGAACTCCTGGTCTC
AAGCAGTCCCCCCACCTCGGCCTCCCAAAGTGCTGGGATAACAGGCGTGAGCCACTGCGCCTGATCCACACACCATAGTTTTTAAAATGTTATTTTACTC
ACAAGAGGGCTTTGGAAAGGAAGATCCTGCCCAGCAGAGCCTACATGCGCAGACAGGACAGAGGACCCTTAAGGATCAATGGTCTTGTTGCCGGAAATGG
ATGTCTGGCGCAACCCCCGGAGCTAGTTTTGGGGAGGCCGCCTTGTTGACTGTGCACTGGAAAATGCACATTGCTTTATCGTGAGCTCTCGGTGCACAGT
GTGGTTTCCAGGCTCTGAGTGGCCAATAAAGCTGGTGCTGTCTT

Loop counts:

4 nts: 1

Tetra-loop variants:

GGGU    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: 1
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: 1
C x U bulge: 0
C x C bulge: 0