Annotated gene sequence

Experiment = in vitro 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

GGTCTCGGCGCCGGAGCCGTTGGCTCCCAGACCCGCCTCTCCGCCTCCTCTCACTTTTCCCAGGGCGGATGCGCCTGCGCTCAGCTGCCTGGGCGGGCTG
GGAGGCGCGGGTTGAAAAGTCTCGTTCCAAGTTTGGAGAGAGAGAGAAGAGCGCCTCAGACCTCGGTACCCGCGAGCGGGGAGGAGGCAGGAAAGAAGGA
CGCGGCGTCTGGGGAGCACCCAGGCAGCAAGACGGGGCCCGGGCTTTCGACAGTGGGGAGTGTGACGCGCTTGGGAAAGGCAGGAGCGCCAGCGGTCGGG
CTGCTCTTGGCTAACGAGAGGAGTCCGAGGCGGCGGCGAGGGGCGAACGACCCGACGCAAGATGGCGAGTAAAGAGATGTTTGAAGATACTGTGGAGGAG
CGTGTCATCAATGAAGAATATAAAATCTGGAAGAAGAATACACCGTTTCTATATGACCTGGTTATGACCCATGCTCTTCAGTGGCCCAGTCTTACCGTTC
AGTGGCTTCCTGAAGTGACTAAACCTGAAGGAAAAGATTATGCCCTTCATTGGCTAGTGCTGGGGACTCATACGTCTGATGAGCAGAATCATCTGGTGGT
TGCTCGAGTACATATTCCCAATGATGATGCACAGTTTGATGCTTCCCATTGTGACAGTGACAAGGGTGAATTTGGTGGCTTTGGTTCTGTAACAGGAAAA
ATTGAATGTGAAATTAAAATCAATCACGAAGGAGAAGTAAACCGTGCTCGTTACATGCCGCAGAATCCTCACATCATTGCTACAAAAACACCATCTTCTG
ATGTGTTGGTTTTTGACTATACAAAACACCCTGCTAAACCAGACCCAAGTGGAGAATGTAATCCTGATCTCAGATTAAGAGGTCACCAGAAGGAAGGCTA
TGGTCTCTCCTGGAATTCAAATTTGAGTGGACATCTCCTAAGTGCATCTGATGACCATACTGTTTGTCTGTGGGATATAAACGCAGGACCAAAAGAAGGC
AAAATTGTGGATGCTAAAGCCATCTTTACTGGCCACTCAGCTGTTGTAGAGGATGTGGCCTGGCACCTGCTGCACGAGTCATTGTTTGGATCTGTTGCTG
ATGATCAGAAACTTATGATATGGGACACCAGGTCCAATACCACCTCCAAGCCGAGTCACTTGGTGGATGCGCACACTGCCGAAGTCAACTGCCTCTCATT
CAATCCCTACAGCGAATTTATTCTAGCCACCGGCTCTGCGGATAAGACCGTAGCTTTATGGGATCTGCGTAACTTAAAATTAAAACTCCATACCTTCGAA
TCTCATAAAGATGAAATTTTCCAGGTCCACTGGTCTCCACATAATGAAACTATTCTGGCTTCAAGTGGTACTGACCGCCGCCTGAATGTGTGGGATTTAA
GTAAAATTGGGGAAGAACAATCAGCAGAAGATGCAGAAGATGGGCCTCCAGAACTCCTGTTTATTCATGGAGGACACACTGCTAAGATTTCAGATTTTAG
CTGGAACCCCAATGAGCCTTGGGTCATTTGCTCAGTGTCTGAGGATAACATCATGCAGATATGGCAAATGGCTGAAAATATTTACAATGATGAAGAGTCA
GATGTCACGACATCCGAACTGGAGGGACAAGGATCTTAAACCCAAAGTACGAGAAATGTTTCTGTTGAATGTAATGCTACATGAATGCTTGATTTATCAA
GCGCCAAAAAGGCATTGTATAGTAGGAAATGTAAGTGGGGTGGCTTATGGCTTCTTTATCCTCTGATTCTAGCACTTTCAAGTGAGCTGTTGCGTACTGT
ATCATATTGTAGCTATTAGGGAAGAGAAGAATGTTGCTTAAGAAAGAACATCACCATTGATTTTAAATACAAGTAGCAGGGTATTGCCTTTGATTCAACT
GTTTTAAGTCCTCATTTTCTCAAACTAAGTGCTTGCTGTTCCCAAATATGCAAGAATAACTTTTACACTTTTTCCTTCCAACACTTCTTGATTGGCTTTG
CAGAAATAAAGTTTTAAAATAAAACTTGTGTTTTTTTAAAAGCTTAGTGGGGGGGGGCGGGGGAGTCTACTTTTTGAGTAGAAATGGGTAAAATGGTACC
TTTGGACTCCTACAGTTAAGGTCACATGGATAATGAAAGAATACACAGAAGCTGTTAAGTTTATCATACATATTTACTTAATCTATACAGAATCAAGTAG
ATAAAATCAGATTCACATTAGTGAAAAATCTCTACAAAATGTCTTTGAAAAGCAAAACGAGACTGCCTCTTAACAATTCGTATCCTCATGAAAGACGTGG
GCTGTAAAAATAAAGCAGTGTGTTTAGCACAAA

Loop counts:

3 nts: 6
4 nts: 6
5 nts: 2
6 nts: 2
7 nts: 2
8 nts: 2

Tetra-loop variants:

UUUA    1
CCAU    1
CCCA    1
CGAG    1
UAUG    1
GGAU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 1
U x 0 bulge: 2
C x 0 bulge: 0

1 x 1 internal loop variants:

G x G bulge: 2
G x A bulge: 0
G x U bulge: 0
G x C bulge: 0
A x G bulge: 0
A x A bulge: 2
A x U bulge: 0
A x C bulge: 1
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: 1
C x U bulge: 0
C x C bulge: 0