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

CATCTTTTACAAGAAACCTTCGCTGCAACCGCTGCGTCACATCACCGCGTCTCCCAGGGACAGGAAAGCCTCTCCGTGTTTGGTGAAGCTTCAGGGGAAG
CAGTCATCCTGTCGTCGCATACGGCAAAATCCTCCATTGCCGTAGCCGTTCGGCTGACGTGACAAGGGAGGTGCAGGCCAACACGGCGACTCCGCGCCCT
CTGGCGGCAGTGCCGGAGCAGCGGCGCTGTCTTTGACCTATCCGGCATTCGGCTTCCGGGACCGCTTGGCGGCTGTGAATGCAGAGCTGGGGCGACGTGG
GGCTCGCTTCCTGGGACTGGGTGTAAAGGGAGAAGATGAGGAAGAGAACAATTTGGAAGTACGTGAAACCAAAATTAAGGGTAAAAGTGGGAGATTCTTC
ACAGTCAAGCTCCCAGTTGCTCTTGATCCTGGGGCCAAGATTTCAGTCATTGTGGAAACAGTCTACACCCATGTGCTTCATCCGTATCCAACCCAGATCA
CCCAGTCAGAGAAACAGTTTGTGGTGTTTGAGGGGAACCATTATTTCTACTCTCCCTATCCAACGAAGACACAAACCATGCGTGTGAAGCTTGCCTCTCG
AAATGTGGAGAGCTACACCAAGCTGGGGAACCCCACGCGCTCTGAGGACCTACTGGATTATGGGCCTTTCAGAGATGTGCCTGCCTATAGTCAGGATACT
TTTAAAGTACATTATGAGAACAACAGCCCTTTCCTGACCATCACCAGCATGACCCGAGTCATTGAAGTCTCTCACTGGGGTAATATTGCTGTGGAAGAAA
ATGTGGACTTAAAGCACACAGGAGCTGTGCTTAAGGGGCCTTTCTCACGCTATGATTACCAGAGACAGCCAGATAGTGGAATATCCTCCATCCGTTCTTT
TAAGACCATCCTTCCTGCTGCTGCCCAGGATGTTTATTACCGGGATGAGATTGGCAATGTTTCTACCAGCCACCTCCTTATTTTGGATGACTCTGTAGAG
ATGGAAATCCGGCCTCGCTTCCCTCTCTTTGGCGGGTGGAAGACCCATTACATCGTTGGCTACAACCTCCCAAGCTATGAGTACCTCTATAATTTGGGTG
ACCAGTATGCACTGAAGATGAGGTTTGTGGACCATGTGTTTGATGAACAAGTGATAGATTCTCTGACTGTGAAGATCATCCTGCCTGAAGGAGCCAAGAA
CATTGAAATTGATAGTCCCTATGAAATCAGCCGTGCCCCAGATGAGCTGCACTACACCTATCTGGACACATTTGGCCGCCCTGTGATTGTTGCCTACAAG
AAAAATCTGGTAGAACAGCACATTCAGGACATTGTGGTCCACTACACGTTCAACAAGGTGCTCATGCTGCAGGAGCCCCTGCTGGTGGTGGCGGCCTTCT
ACATCCTGTTCTTCACCGTTATCATCTATGTTCGGCTGGACTTCTCCATCACCAAGGATCCAGCCGCAGAAGCCAGGATGAAGGTAGCCTGCATCACAGA
GCAGGTCTTGACCCTGGTCAACAAGAGAATAGGCCTTTACCGTCACTTTGACGAGACCGTCAATAGGTACAAGCAATCCCGGGACATCTCCACCCTCAAC
AGTGGCAAGAAGAGCCTGGAGACTGAACACAAGGCCTTGACCAGTGAGATTGCACTGCTGCAGTCCAGGCTGAAGACAGAGGGCTCTGATCTGTGCGACA
GAGTGAGCGAAATGCAGAAGCTGGATGCACAGGTCAAGGAGCTGGTGCTGAAGTCGGCGGTGGAGGCTGAGCGCCTGGTGGCTGGCAAGCTCAAGAAAGA
CACGTACATTGAGAATGAGAAGCTCATCTCAGGAAAGCGCCAGGAGCTGGTCACCAAGATCGACCACATCCTGGATGCCCTGTAGCCCCTGCCCGCATCC
TCCAGGGGGCCCAGGGTGCCTGCACTTTGCTGTGGCAGGCAGATTGGGTGGTAGTGGGAGGTTGTGCATGGAGGCCAGTGAAAGCTGACATCTGTAAAAG
GCCTTCAAGGAAGAGAAACCAGGCCCTGCGTCAGGCAGTGTGAGTTTGCCGTTTGTCCTTAACTTTCTTTTTTTTTTTTTTTAAAAAAAGAAAACTTTAA
AAAAACTCCCATTAAAAACAAAACATCTTTGTGTTTT

Loop counts:

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

Tetra-loop variants:

AGAC    1
CUGC    1
CUUU    1
AAAA    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: 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