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

AGTGCGGCCGCCGCCGCCACAGCTGCAGTCAGCACCGTCACCCCAGCAGCATCCGCCGCCTGCACCGCGCGTGCGGCCCGCCCCGGCCTGACCCCGCCGC
CGAACCCGGCGCCAGCCATGGAGCCCGAAGCCCCCCGTCGCCGCCACACCCATCAGCGCGGCTACCTGCTGACACGGAACCCTCACCTCAACAAGGACTT
GGCCTTTACCCTGGAAGAGAGACAGCAATTGAACATTCATGGATTGTTGCCACCTTCCTTCAACAGTCAGGAGATCCAGGTTCTTAGAGTAGTAAAAAAT
TTCGAGCATCTGAACTCTGACTTTGACAGGTATCTTCTCTTAATGGATCTCCAAGATAGAAATGAAAAACTCTTTTATAGAGTGCTGACATCTGACATTG
AGAAATTCATGCCTATTGTTTATACTCCCACTGTGGGTCTGGCTTGCCAACAATATAGTTTGGTGTTTCGGAAGCCAAGAGGTCTCTTTATTACTATCCA
CGATCGAGGGCATATTGCTTCAGTTCTCAATGCATGGCCAGAAGATGTCATCAAGGCCATTGTGGTGACTGATGGAGAGCGTATTCTTGGCTTGGGAGAC
CTTGGCTGTAATGGAATGGGCATCCCTGTGGGTAAATTGGCTCTATATACAGCTTGCGGAGGGATGAATCCTCAAGAATGTCTGCCTGTCATTCTGGATG
TGGGAACCGAAAATGAGGAGTTACTTAAAGATCCACTCTACATTGGACTACGGCAGAGAAGAGTAAGAGGTTCTGAATATGATGATTTTTTGGACGAATT
CATGGAGGCAGTTTCTTCCAAGTATGGCATGAATTGCCTTATTCAGTTTGAAGATTTTGCCAATGTGAATGCATTTCGTCTCCTGAACAAGTATCGAAAC
CAGTATTGCACATTCAATGATGATATTCAAGGAACAGCATCTGTTGCAGTTGCAGGTCTCCTTGCAGCTCTTCGAATAACCAAGAACAAACTGTCTGATC
AAACAATACTATTCCAAGGAGCTGGAGAGGCTGCCCTAGGGATTGCACACCTGATTGTGATGGCCTTGGAAAAAGAAGGTTTACCAAAAGAGAAAGCCAT
CAAAAAGATATGGCTGGTTGATTCAAAAGGATTAATAGTTAAGGGACGTGCTTCCTTAACACAAGAGAAAGAGAAGTTTGCCCATGAACATGAAGAAATG
AAGAACCTAGAAGCCATTGTTCAAGAAATAAAACCAACTGCCCTCATAGGAGTTGCTGCAATTGGTGGTGCATTCTCAGAACAAATTCTCAAAGATATGG
CTGCCTTCAATGAACGGCCTATTATTTTTGCTTTGAGTAATCCAACTAGCAAAGCAGAATGTTCTGCAGAGCAGTGCTACAAAATAACCAAGGGACGTGC
AATTTTTGCCAGTGGCAGTCCTTTTGATCCAGTCACTCTTCCAAATGGACAGACCCTATATCCTGGCCAAGGCAACAATTCCTATGTGTTCCCTGGAGTT
GCTCTTGGTGTTGTGGCGTGTGGATTGAGGCAGATCACAGATAATATTTTCCTCACTACTGCTGAGGTTATAGCTCAGCAAGTGTCAGATAAACACTTGG
AAGAGGGTCGGCTTTATCCTCCTTTGAATACCATTAGAGATGTTTCTCTGAAAATTGCAGAAAAGATTGTGAAAGATGCATACCAAGAAAAGACAGCCAC
AGTTTATCCTGAACCGCAAAACAAAGAAGCATTTGTCCGCTCCCAGATGTATAGTACTGATTATGACCAGATTCTACCTGATTGTTATTCTTGGCCTGAA
GAGGTGCAGAAAATACAGACCAAAGTTGACCAGTAGGATAATAGCAAACATTTCTAACTCTATTAATGAGGTCTTTAAACCTTTCATAATTTTTAAAGGT
TGGAATCTTTTATAATGATTCATAAGACACTTAGATTAAGATTTTACTTTAACAGTCTAAAAATTGATAGAAGAATATCGATATAAATTGGGATAAACAT
CACATGAGACAATTTTGCTTCACTTTGCCTTCTGGTTATTTATGGTTTCTGTCTGAATTATTCTGCCTACGTTCTCTTTAAAAGCTGTTGTACGTACTAC
GGAGAAACTCATCATTTTTATACAGGACACTAATGGGAAGACCAAAATTACTAATAAATTGACATAACCAACATTAAAACTCATAATTATTTTGTTGACC
ATTTTGTTAAAATCTACTTTTCAAAAAAAAAAAGCTAGAAATGAATCTAGGCGTAGGTGAACTTTTGCTAAGCAGAAATAACACTACTTTGTTGCCTAGA
GAAAGATAACTTCTCAAGTATTTTTATTCCAGTCCTAGATCATATATGTTCTTTTGTGCAACGGAATTCTAACAGTTCTAAGAGAAAGATCACTGCTGTT
TACAGCGCCTTGTGCAGCCTTAGATTTTAATATTCTTTTGTCATTGTTACATCTCATAGAGTAAAGCTCTTATTACCTTGATCCTGAGTCAGAAATCCCA
CCTGAAATCACCTTTTTTCCCCCTTGATCAAACATCCCATCCTTCAGCTACCATACTGTTGCTACAGGGATTTTGTGGACTGTGGCCCCTGTCCCGAGGT
TGGCACCTTCAGTTCAGCACAGCCTGAGCAGTGAGAAGGTCTGAAAGGAGAGTATATAGTTAAGATCCTTGAGAAAGGGCTGCCTGAGGAACTGACCTCT
TAAAGATCTCAGGATCTTTAAGACAACAAGTTAGGTTCCTACTGGAGTTACCTGCCAGAATGGCCTCTTAATTAACTCAGGTAATGAAGAGCTAACTGTG
TTATAATCATCTTGCTTTTGCCTGAATTTGGAGAAAGTATTATAATTAAGTTCCCAGTATCAGAAATGTCCTTACATAAGATTAAAATATCTTGATGACT
AATACCATTCTATGAGAAAGAGTAGTTATATGCCCAGACTGTATTAATTTACTTTAGAAACTAATGTTTGAAGTAATGGAAAAAATTTTAAATTATAAAG
CTAAGGTGCAATAACATTTGCTACTTATTTATAGAATTATTTGAAGAATTTTGTTTTTGAAGTAATGCTTTAAGGAGTATAAGATATTCAAGATAAATTA
TACTATAAAATGATTTTATTGAAAGTTGAAGGTTACACAAATTGTTTTAGGTATGAGCAGAAGAGGTTAAGGTATTTCTAAAGGTAACATATAGTCAAGA
GTTTCCTCAAAATAGTTATTTGGAGAAGAATCAGAATGTCTGTGTATTTCTTGTCTGTTTCTATGTTGTCTTATAGCTCTGACTAAATGTGTTTACCTAT
GCAAAAGATTTATTAAAGCATAGAAAAGGTGAATGAATAAAAATATAAAATAATTGTCCTTTTTCTTAAAA

Loop counts:

10 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