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

AGCGTTCTCTTCCGCCGTCGTCGCCGCCATCCTCGGCGCGACTCGCTTCTTTCGGTTCTACCTGGGAGAATCCACCGCCATCCGCCACCATGGTGAACTT
CACGGTAGACCAGATCCGCGCCATCATGGACAAGAAGGCCAACATCCGCAACATGTCTGTCATCGCCCACGTGGACCATGGCAAGTCCACGCTGACAGAC
TCCCTGGTGTGCAAGGCGGGCATCATCGCCTCGGCCCGGGCCGGGGAGACACGCTTCACTGATACCCGGAAGGACGAGCAGGAGCGTTGCATCACCATCA
AGTCAACTGCCATCTCCCTCTTCTACGAGCTCTCGGAGAATGACTTGAACTTCATCAAGCAGAGCAAGGACGGTGCCGGCTTCCTCATCAACCTCATTGA
CTCCCCCGGGCATGTCGACTTCTCCTCGGAGGTGACTGCTGCCCTCCGAGTCACCGATGGCGCATTGGTGGTGGTGGACTGCGTGTCAGGCGTGTGCGTG
CAGACGGAGACAGTGCTGCGGCAGGCCATTGCCGAGCGCATCAAGCCTGTGCTGATGATGAACAAGATGGACCGCGCCCTGCTGGAGCTGCAGCTGGAGC
CCGAGGAGCTCTACCAGACTTTCCAGCGCATCGTGGAGAACGTGAACGTCATCATCTCCACCTACGGCGAGGGCGAGAGCGGCCCCATGGGCAACATCAT
GATCGATCCTGTCCTCGGTACCGTGGGCTTTGGGTCTGGCCTCCACGGGTGGGCCTTCACCCTGAAGCAGTTTGCCGAGATGTATGTGGCCAAGTTCGCC
GCCAAGGGGGAGGGCCAGTTGGGGCCTGCCGAGCGGGCCAAGAAAGTAGAGGACATGATGAAGAAGCTGTGGGGTGACAGGTACTTTGACCCAGCCAACG
GCAAGTTCAGCAAGTCAGCCACCAGCCCCGAAGGGAAGAAGCTGCCACGCACCTTCTGCCAGCTGATCCTGGACCCCATCTTCAAGGTGTTTGATGCGAT
CATGAATTTCAAGAAAGAGGAGACAGCAAAACTGATAGAGAAACTGGACATCAAACTGGACAGCGAGGACAAGGACAAAGAAGGCAAACCCCTGCTGAAG
GCTGTGATGCGCCGCTGGCTGCCTGCCGGAGACGCCTTGTTGCAGATGATCACCATCCACCTGCCCTCCCCTGTGACGGCCCAGAAGTACCGCTGCGAGC
TCCTGTACGAGGGGCCCCCGGACGACGAGGCTGCCATGGGCATTAAAAGCTGTGACCCCAAAGGCCCTCTTATGATGTATATTTCCAAAATGGTGCCAAC
CTCCGACAAAGGTCGGTTCTACGCCTTTGGACGAGTCTTCTCGGGGCTGGTCTCCACTGGCCTGAAGGTCAGGATCATGGGGCCCAACTATACCCCTGGG
AAGAAGGAGGACCTCTACCTGAAGCCAATCCAGAGAACAATCTTGATGATGGGCCGCTACGTGGAGCCCATCGAGGATGTGCCTTGTGGGAACATTGTGG
GCCTCGTGGGCGTGGACCAGTTCCTGGTGAAGACGGGCACCATCACCACCTTCGAGCACGCGCACAACATGCGGGTGATGAAGTTCAGCGTCAGCCCTGT
TGTCAGAGTGGCCGTGGAGGCCAAGAACCCGGCTGACCTGCCCAAGCTGGTGGAGGGGCTGAAGCGGCTGGCCAAGTCCGACCCCATGGTGCAGTGCATC
ATCGAGGAGTCGGGAGAGCATATCATCGCGGGCGCCGGCGAGCTGCACCTGGAGATCTGCCTGAAGGACCTGGAGGAGGACCACGCCTGCATCCCCATCA
AGAAATCTGACCCGGTCGTCTCGTACCGCGAGACGGTCAGTGAAGAGTCGAACGTGCTCTGCCTCTCCAAGTCCCCCAACAAGCACAACCGGCTGTACAT
GAAGGCGCGGCCCTTCCCCGACGGCCTGGCCGAGGACATCGATAAAGGCGAGGTGTCCGCCCGTCAGGAGCTCAAGCAGCGGGCGCGCTACCTGGCCGAG
AAGTACGAGTGGGACGTGGCTGAGGCCCGCAAGATCTGGTGCTTTGGGCCCGACGGCACCGGCCCCAACATCCTCACCGACATCACCAAGGGTGTGCAGT
ACCTCAACGAGATCAAGGACAGTGTGGTGGCCGGCTTCCAGTGGGCCACCAAGGAGGGCGCACTGTGTGAGGAGAACATGCGGGGTGTGCGCTTCGACGT
CCACGACGTCACCCTGCACGCCGACGCCATCCACCGCGGAGGGGGCCAGATCATCCCCACAGCACGGCGCTGCCTCTATGCCAGTGTGCTGACCGCCCAG
CCACGCCTCATGGAGCCCATCTACCTTGTGGAGATCCAGTGTCCAGAGCAGGTGGTCGGTGGCATCTACGGGGTTTTGAACAGGAAGCGGGGCCACGTGT
TCGAGGAGTCCCAGGTGGCCGGCACCCCCATGTTTGTGGTCAAGGCCTATCTGCCCGTCAACGAGTCCTTTGGCTTCACCGCTGACCTGAGGTCCAACAC
GGGCGGCCAGGCGTTCCCCCAGTGTGTGTTTGACCACTGGCAGATCCTGCCCGGAGACCCCTTCGACAACAGCAGCCGCCCCAGCCAGGTGGTGGCGGAG
ACCCGCAAGCGCAAGGGCCTGAAAGAAGGCATCCCTGCCCTGGACAACTTCCTGGACAAATTGTAGGCGGCCCTTCCTGCAGCGCCTGCCGCCCCGGGGA
CTCGCAGCACCCACAGCACCACGTCCTCGAATTCTCAGACGACACCTGGAGACTGTCCCGACACAGCGACGCTCCCCTGAGAGGTTTCTGGGGCCCGCTG
CGTGCCATCACTCAACCATAACACTTGATGCCGTTTCTTTCAATATTTATTTCCAGAGTCCGGAGGCAGCAGACACGCCCTCTTAGTAGGGACTTAATGG
GCCGGTCGGGGAGGGGGAGGCGGGATGGGACACCCAACACTTTTTCCATTTCTTCAGAGGGAAACTCAGATGTCCAAACTAATTTTAACAAACGCATTAA
GAGGTTTATTTGGGTACATGGCCCGCAGTGGCTTTTGCCCCAGAAAGGGGAAAGGAACACGCGGGTAGATGATTTCTAGCAGGCAGGAAGTCCTGTGCGG
TGTCACCATGAGCACCTCCAGCTGTACTAGTGCCATTGGAATAATAAATTTGATAAGGTGGTGA

Loop counts:

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

Tetra-loop variants:

UGAA    1
UCAA    1
CCUC    1
ACCC    1
AGAC    1
AAGU    1
GCCA    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 0
U x 0 bulge: 3
C x 0 bulge: 1

1 x 1 internal loop variants:

G x G bulge: 1
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: 2