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

GCCGGCACCATGAGTGAACAGAGTATCTGTCAGGCAAGAGCTGCTGTGATGGTTTATGATGATGCCAATAAGAAGTGGGTGCCAGCTGGTGGCTCAACTG
GATTCAGCAGAGTTCATATCTATCACCATACAGGCAACAACACATTCAGAGTGGTGGGCAGGAAGATTCAGGACCATCAGGTCGTGATAAACTGTGCCAT
TCCTAAAGGGTTGAAGTACAATCAAGCTACACAGACCTTCCACCAGTGGCGAGATGCTAGACAGGTGTATGGTCTCAACTTTGGCAGCAAAGAGGATGCC
AATGTCTTCGCAAGTGCCATGATGCATGCCTTAGAAGTGTTAAATTCACAGGAAACAGTGTTCTATTTAGGGCCAACATTGCCTAGACAAAACTCACAAC
TACCTGCTCAAGTTCAAAATGGCCCATCCCAAGAAGAATTGGAAATTCAAAGAAGACAACTACAAGAACAGCAACGGCAAAAGGAGCTGGAGCGGGAAAG
GCTGGAGCGAGAAAGAATGGAAAGAGAAAGGTTGGAGAGAGAGAGGTTAGAAAGGGAAAGGCTGGAGAGGGAGCGACTGGAACAAGAACAGCTGGAGAGA
GAGAGACAAGAACGGGAACGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGAGCGGCAGGAACGCCTGGATCGGGAGAGGC
AAGAAAGACAAGAACGAGAGAGGCTGGAGAGACTGGAACGGGAGAGGCAAGAAAGGGAGCGACAAGAGCAGTTAGAAAGGGAACAGCTGGAATGGGAGAG
AGAGCGCAGAATATCAAGTGCTGCTCCATCTTCAGACAGCTCCCTGTATAACGCTCCACTTCCTGAGTATTCCAGTTGCCAGCCTCCTTCAGCACCTCCT
CCATCATACGCTAAAGTCATCTCAGCTCCAGTGTCAGATGCCACTCCTGATTATGCTGTAGTGACTGCTTTGCCACCTACTTCCACACCCCCTACACCAC
CACTGCGACACTCAGCGACACGTTTTGCAACATCTTTAGGTTCAGCCTTCCACCCTGTTCTTCCCCATTACGCTACAGTTCCTCGTCCTCTGAACAAAAA
CTCTCGACCTTCTTCTCCTGTGAACACACCCTCTTCTCAGCCTCCAGCTACGAAGCCCTGTGCCTGGTCTACTTCCAATTTTTCGCCCCTCCCTCCATCT
CCTCCAATAATGATTAGCAGCCCCCCAGGCAAAGCTACTGGTCCAAGGCCTGTCCTCCCTGTTTGTGTTTCTTCTCCTGTGCCCCAAATGCCTCCATCAC
CGACAGCACCCAATGGGCTGGTTGACTCTGTAACATATCCAGTGTCTCCACCGCCTACCTCAGGGCCAGCAGCTCCTCCGCCGCCGCCTCCACTGCCTTC
CCTCGCATCACTCTCACACTGTGGATCTCAAGCTTCTCCTCCTCCAAGCACCCCTATTGCCTCAACTCCCTCATCCAAGCCTAGTGTTCTCCCTTCTCCC
TCTGCAGCTGCCCCTGCCTCTGTTGAGACTCCTCTAAACTCTGTGCTGGGAGACTCTTCTGCTTCTGAGCCAGGCTTGCAGGCAGCCTCTCAGCCGGCCG
AGACTCCATCCCAACAGGGCATTGTCTTGGGACCACTTGCACCTCCACCTCCTCCACCACTCCCACCAGGGCCTGCACAGGCTTCAGTAGCCCTCCCTCC
TCCCCCAGGGCCCCCTCCACCTCCTCCACTCCCATCCACCGGGCCTCCACCGCCCCCTCCTCCCCCTCCTCTCCCTAATCAAGTACCCCCTCCTCCTCCA
CCACCTCCTGCCCCACCCCTCCCTGCATCTGGATTCTTTTTGGCATCCATGTCAGAAGACAATCGCCCTTTAACTGGACTTGCAGCTGCAATTGCCGGAG
CAAAACTTAGGAAAGTGTCACGGATGGAGGATACCTCTTTCCCAAGTGGAGGGAATGCTATTGGTGTGAACTCCGCCTCATCTAAAACAGATACAGGCCG
TGGAAATGGACCCCTTCCTTTAGGGGGTAGTGGTTTAATGGAAGAAATGAGTGCCCTGCTGGCCAGGAGGAGAAGAATTGCTGAAAAGGGATCAACAATA
GAAACAGAACAAAAAGAGGACAAAGGTGAAGATTCAGAGCCTGTAACTTCTAAGGCCTCTTCAACAAGTACACCTGAACCAACAAGAAAACCTTGGGAAA
GAACAAATACAATGAATGGCAGCAAGTCACCTGTTATCTCCAGACCAAAATCCACACCCTTATCACAGCCCAGTGCCAATGGAGTCCAGACGGAAGGACT
TGACTATGACAGGCTGAAGCAGGACATTTTAGATGAAATGAGAAAAGAATTAACAAAGCTAAAAGAAGAGCTCATTGATGCAATCAGGCAGGAACTGAGC
AAGTCAAATACTGCATAGAGGAACAGACTAAGGAGAGATAGGACTTTAATCTGGAGGAAAAATATCCTACAAACAACAACTGTTCACAACAGCAAACCCC
TACATTTATGAGCTGTAAGAAGAAAATGGAGACAAACAGAAGGAGGGAAAAACCAACCTACTCTGAAAGCCTTCAGACATTATGACTCTGGTGATAAGCT
CTTTCCCTCTCCGTTTGCTGCTTTTTTCTGGCCTTTACAACAGAATGGAAGAGAATCATTTAAGAGTTCCTGTAACAGTTATGCAGAAAATACTAAAACC
CATCAGGCAAGATCACCACGCATTGAAATATTTTCATATCAAGATAAAGTCGCACATTTTCCACAATACATTGCTAAAATAAAGAGGAGAAAGGCTTAGG
AAGTTTTTTTGCAGAGAGTGCTGGTAAAGAATTGAGCAAGTTTGCTATTGTATTGTAATGTTTCTCTCAGGTTTGTTCTTCCTATCATGTTTGATATTCC
ATGAATAATTGAGATCAGCCCTATGTAAGTTAAGATCATAATATGTGGAACAAATGGAATTGTAAGTGCTTTCAAAGGGTAATATTTATAAGAAAGTGTC
CGAAAAATGTTTCTTCAGCTTGAGAAATTTTAGAATGATAGGAAGTTTCTCGAGTTAGCCTTCATGCAATTTTGTAGATTAAAACATAAAATTTGTCCAG
AACTTAAAGATTTAGATGCCTTCCTAAATTGTTACAATGCTTTACCAAATCTATGACTTCTACATAACACAAACCAGTGGTCAAATGTAAACACTATATT
GTAGATTTACTGTAGGTTTTCAACCTTTTTTAGATTTATGCATGTGGACATTTTTATAATGTAATTACAATCACCACAAGGTTAGCTTTTTTAATTGCAG
ACAGTAAT

Loop counts:

5 nts: 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