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

AGGCGTCTGAGGGGCGGACGGAGGCGGCGGCGGCGGCGGCGGGAGCGGGAGCGGGCGGCGAGTGGGGAGCGGGGCCGGGAGTGGAGCAGCCGCCGCGGCG
GGACTGGACCGAGCCTCGCCGGCGCGCACCTGCCCGCAGCGCCCGCGGAGCGCGCAGCGCGGCCCGAGCGCGACGACCTGCCGAGCGGCGGCCGAGGCGG
CGGTGTGGGCGCGTCAGGCCGCGACGAGGGCGCTGAGACAAATTTACATGTATTGGAGACCAGACCAGAAGCCCTTCTGAATTAAGATCTCACATTCTTG
AAGGTGGCATTGAAGAGCACTAAGATCGGAAGATGAGTGAGCTTGACCAGTTACGGCAGGAGGCCGAGCAACTTAAGAACCAGATTCGAGACGCCAGGAA
AGCATGTGCAGATGCAACTCTCTCTCAGATCACAAACAACATCGACCCAGTGGGAAGAATCCAAATGCGCACGAGGAGGACACTGCGGGGGCACCTGGCC
AAGATCTACGCCATGCACTGGGGCACAGACTCCAGGCTTCTCGTCAGTGCCTCGCAGGATGGTAAACTTATCATCTGGGACAGCTACACCACCAACAAGG
TCCACGCCATCCCTCTGCGCTCCTCCTGGGTCATGACCTGTGCATATGCCCCTTCTGGGAACTATGTGGCCTGCGGTGGCCTGGATAACATTTGCTCCAT
TTACAATCTGAAAACTCGTGAGGGGAACGTGCGCGTGAGTCGTGAGCTGGCAGGACACACAGGTTACCTGTCCTGCTGCCGATTCCTGGATGACAATCAG
ATCGTCACCAGCTCTGGAGACACCACGTGTGCCCTGTGGGACATCGAGACCGGCCAGCAGACGACCACGTTTACCGGACACACTGGAGATGTCATGAGCC
TTTCTCTTGCTCCTGACACCAGACTGTTCGTCTCTGGTGCTTGTGATGCTTCAGCCAAACTCTGGGATGTGCGAGAAGGCATGTGCCGGCAGACCTTCAC
TGGCCACGAGTCTGACATCAATGCCATTTGCTTCTTTCCAAATGGCAATGCATTTGCCACTGGCTCAGACGACGCCACCTGCAGGCTGTTTGACCTTCGT
GCTGACCAGGAGCTCATGACTTACTCCCATGACAACATCATCTGCGGGATCACCTCTGTCTCCTTCTCCAAGAGCGGGCGCCTCCTCCTTGCTGGGTACG
ACGACTTCAACTGCAACGTCTGGGATGCACTCAAAGCCGACCGGGCAGGTGTCTTGGCTGGGCATGACAACCGCGTCAGCTGCCTGGGCGTGACTGACGA
TGGCATGGCTGTGGCGACAGGGTCCTGGGATAGCTTCCTCAAGATCTGGAACTAACGCCAGTAGCATGTGGATGCCATGGAGACTGGAAGACCATTCCAA
CTTGGACGCGTTACCATGAGAGCATATCCTATCCAACCGTACTAACGTGGACACCCTACACCTCCCCTCAGAACTTCAAAAGGGCAAGATCTTTTTTCCT
TCACTTATTGCTGAAACCAAGAGCACAATTCCCATTGAGAGAAAGATCTCTGTGCTGTAAACTAAAACAAATTGTGCATTCCTTCCGGGGCCATCGTCTT
TGTTTTCTTTTTTGTCTTGAATGAATTTTAAAAGGAAATATATAATAAAAATGTTAACCAGAAGGTAAACTTGAGTGTAATTGTCAGACAGACACACTTT
TCCACCAGTGTATTTGAATTTTAGACCAGTGACCCTGTTTTGTGGCATTCATGCAAAACATGCTGAGGGCTTTGTTCATCTGGTCATCGTGTCCAAATTT
CAGTCATGTTTGTAGCAAGATTTTGGAAGCATTCATATTTCCTTTTTAAAATGTATTCCTTTGTGTTCAACAGTTAATCAAAACCAGAGAGTCTAGGGCA
GCCTCTCTGATGTTGTCAATGATGTAAATTCAGTCCCTGGTTTTTAATTTTCTGTCTGATGTCACAGATCATTGTTGCACACAAACGTGGCATAGAAAAG
AACATGTTCAGAAGCCATGGGGCCAAGCACATGCGGGGACGGTCTCAAATGCGTGATCAGAGAATCCTTCACCTTTGCTGAAAAGTGAGCTCAGATCCAG
CACCATGTTCCTCCTGACCCATCCTGTCTATCTTCTCAGTTGAGTTTTTAATCTCACTTTGGGTTTCCTTGTGAAGTTGGAGGGAAGTTTATAATAGCCT
AACACTACCCCACCCCCAACTAGGAGGAACCTCTGTTTTCAAGAGAGATGCCTGTCCTGTGCTTGGATAGTCAGTCAATTATTTGTGTATGAAACAATGT
ACAAATCAATGTTTTGAAAATAATGATCTCAGACTTTCTAAGTTAAATTTTAAAAATTTTGATTGTTTGCCATATTGGGTGGGTTTACTCTTAGAATCGC
ATGCTGTAGAAATGCTCAAAAGTGCATATGGGACTCAGTCCTTAGGTGTTCTTTTTCTTTTAAGAAATAACCTCTTACAGTTGTAACCATTGCGGCTCTG
TCCACTTCTCGTTGCTGCTCTGTGGCACATATCGGAAGCAGTACAGCGCGCGGCTCTACACGCTTGGGTAGCGGGATAAGTCACTGTTTTCTTTATTTCT
TTAAAAAAAAAAAAGTTCTGTTGCAAACGACTGCTGTTGGATTCTGAGGGTGGGGAGGGAGAGAGAGGGAGGGAGAGGGAGTGAAGAGCCTGCCCTCCTA
TATGGATTCTTCAGGGCCCTCCACATCTGAGGTGGCTCATTCCCATCACACACAGATTGTCCTGGTGTTCATTTCAAGGCCAGTGTTCAGCAGCAGCGTT
TGGAAAGCAGGTTCTGTGGGACCCCCCGCCCCGCCCCCCGCACTCCTTCATAGCAGCAGTAGTGGCTTCTCCATCCTGTTTTCTGCAACATTCTATACAA
AACTGTGCTGTGACCTTGCGGTAGGCCTGGATCTGGCAAAGAGAATACAAATGAAACCCCTTCTTTCTCTTTCCGTCCAACAACTCTGTAGAGCTCTCTG
CACCCTTACCCCTTTCCACCTTTTGTATTTAATTTTAAAGTCAGTGTACTGCAAGGAAGCTGGATGCAAGATAGATACTATATTAAACTGTACTGTTATT
TAAGATGTAATAAAGCAGTTTGACATGAGGGA

Loop counts:

7 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: 1
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