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

GGTGTGATCTCGGCTCACTGAAACCTCTGCCTCCTAGGTTCAAGCGATTTTCCCATGTCAGCCTCCCCAGTAGCTGGGATTACAGGCGCACGGCACCACG
CCCGGCTAATTTTTCTATTTTATGGTAGAAACGGGATATCACCATGTTGGCCAGGCTGGTGTCAAACTGCTGACCTCAAATGATCCGCCCTCCTCGGCCT
CCCAAAGTGCTGGGATTACAGGTGTGAGCCAAGGTGCCCGACCTGATGTGCTTGTAAGAATTTAAATGAAGAGGGTCAGTCAGCTTAGGAGACGAGGTTA
GATGTAAGGATTTCAGACTTGTCAGTATACAGGTGGTGATTGATGCCGTAGGAATGACTGGTATTACCCAGGGAGCTGGTGCAAAGTAGGAGCCTTGGGG
AACATGTTAAGGGGATGTGAGAGTAAGCCCACAAAGACTCAGAAGTGGCCAGGGAGTAAGGGGAAAATGGGATAGAATAGAGCAAAAGCCACGGGAGGCA
TTCCTTGAATTCCTTGGACTCAGATATGTTAGGGGACAGGAAACACATTGAAGACAACTGAAGAGACTTCAGTGTGCTGCTGAGTTCTTAGCAGAGTAGA
CAGCTGATTTCACCACTATTCCAGACCCTAAAGATTTCTCCTGAAATTGCACTGTTATGCAATTTTTTTCCTTCTCTATTGCCCCACCTCTGGGGCCTAC
ACTCTTTACCTTCTCTGATTTATCTGACCCATCCGCATATCTCTGCAAAGTCTTAATGTAGGTTTCCAGGATTTAATGATTCTTTCAATCAACTTTAAAG
TTCTTCAGGAAGATTCTCCAGGTCCGTCAACAGTTTTCCCCTTCATGACTTTGTGACAAAGCTTTCTTGTTCCACTATCCAGGTGTTCCCAACAAGTTGC
TGTAACGGTGGCCCCTCATAAGCTTGCCTGGAAACCCTAGAAAGCTCAGAAAAATTATGAACTTTGCCCAGTAAGAGGCTGGGAAGTCAGAAAGGGTTTT
AAACAAAACTGACCCCACTTGTTACATGCTCCTTTCACTGTCCAAACGTCAACCAAAGGAACTTTTGTGACGCTAAGACGCTCCCGGCGTCCTCACCCGT
TCACAGCCAGAGTTGATCTTAGAAGGCAGGGGGCTCGCACCGAGACGCTCCTAGCAAGCCCCTCACGCGAGCGAATGACTGGCGCCAGGAGAAACGCATA
GGACCTCCCGAAGCCGCCGAGAGCAAAAGGACCCATCAGAGCTGTGCTGAGACCCGCCGCGGGCCGGGCTCGCACTCGAGATTCTCGCCCGTGGGATTCC
AGTCCTGAGCTGAACGAGAGATAAGTCTTTGTCACCCCCCAGTCTTTACTGTTTCGAGAAACCCTAAGATTTTTTAAAAAAAAGCCCAAGACGTCAAGTC
GGGGAACTCCAACATTGGGGTGTCCAGAAACACTGGGGTTTCAGGCGCTCTGTAAATGCGTCCGAGGTCCGCGGTTCTGCCCGCAAGCCCAGACCCCGGC
CTCACTTCCGCCCCGCGCCCCGCGCCCCGGCCTCACTTCCGCCCCGCGCCCCGCGCCCCGCGCCCCGCGCGCCTCCGCCCGCCCCTGCTCCGGCCTTGCG
CCTGCGCACAGTGGGATGCGCGGGGAGGTGGTGCGCGGGGAGGTGGAGGGCGAGGGGCGGGGCTACCTCAGGTCCCGCCCGCGGCAGGCCTGTGGGCTGC
GAGGAGGAGCTTTGCCTAGCTTGCAGGCAGCGCAGGGCAGACGGCGGCAGGAGAAGCAAGATGAATGCAGGCTCAGATCCTGTGGTCATCGTCTCGGCGG
CGCGGACCATCATAGGTTCCTTCAATGGTGCCTTAGCTGCTGTTCCTGTCCAGGACCTGGGCTCCACTGTCATCAAAGAAGTCTTGAAGAGGGCCACTGT
GGCTCCGGAAGATGTGTCTGAGGTCATCTTTGGACATGTCTTGGCAGCAGGCTGTGGGCAGAATCCTGTTAGACAAGCCAGTGTGGGTGCAGGAATTCCC
TACTCTGTTCCAGCATGGAGCTGCCAGATGATCTGTGGGTCAGGCCTAAAAGCTGTGTGCCTTGCAGTCCAGTCAATAGGGATAGGAGACTCCAGCATTG
TGGTTGCAGGAGGCATGGAAAATATGAGCAAGGCTCCTCACTTGGCTTACTTGAGAACAGGAGTAAAGATAGGTGAGATGCCACTGACTGACAGTATACT
CTGTGATGGTCTTACAGATGCATTTCACAACTGTCATATGGGTATTACAGCTGAAAATGTAGCCAAAAAATGGCAAGTGAGTAGAGAAGATCAGGACAAG
GTTGCAGTTCTGTCCCAGAACAGGACAGAGAATGCACAGAAAGCTGGCCATTTTGACAAAGAGATTGTACCAGTTTTGGTGTCAACTAGAAAAGGTCTTA
TTGAAGTTAAAACAGATGAGTTTCCTCGCCATGGGAGCAACATAGAAGCCATGTCCAAGCTAAAGCCTTACTTTCTTACTGATGGAACGGGAACAGTCAC
CCCAGCCAATGCTTCAGGAATAAATGATGGTGCTGCAGCTGTCGTTCTTATGAAGAAGTCAGAAGCTGATAAACGTGGGCTTACACCTTTAGCACGGATA
GTTTCCTGGTCCCAAGTGGGTGTGGAGCCTTCCATTATGGGAATAGGACCAATTCCAGCCATAAAGCAAGCTGTTACAAAAGCAGGTTGGTCACTGGAAG
ATGTTGACATATTTGAAATCAATGAAGCCTTTGCAGCTGTCTCTGCTGCAATAGTTAAAGAACTTGGATTAAACCCAGAGAAGGTCAATATTGAAGGAGG
GGCTATAGCCTTGGGCCACCCTCTTGGAGCATCTGGCTGTCGAATTCTTGTGACCCTGTTACACACACTGGAGAGAATGGGCAGAAGTCGTGGTGTTGCA
GCCCTGTGCATTGGGGGTGGGATGGGAATAGCAATGTGTGTTCAGAGAGAATGAATTGCTTAAACTTTGAACAACCTCAATTTCTTTTTAAACTAATAAA
GTACTAGGTTGCAATATGTGAAATCAGAGGACCAAAGTACAGATGGAAACCATTTCCTACATCACAAAAACCCAAGTTTACAGCTTGTACTTTACTTTAA
TGTGTAATACTCAACTCAAGGTACAAGACAATTGCATTTAACATTGTTATAAATAAAAGGAACATCAGATCAATCATTAA

Loop counts:

3 nts: 1
4 nts: 2
5 nts: 3
7 nts: 4
8 nts: 1

Tetra-loop variants:

UAUA    1
UCAU    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: 1
G x A bulge: 1
G x U bulge: 0
G x C bulge: 0
A x G bulge: 1
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