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

ACAGCCGCCCAGAAATTCTACCCAAGCTCCCTCAGCACCATGTACCGAGCACTTCGGCTCCTCGCGCGCTCGCGTCCCCTCGTGCGGGCTCCAGCCGCAG
CCTTAGCTTCGGCTCCCGGCTTGGGTGGCGCGGCCGTGCCCTCGTTTTGGCCTCCGAACGCGGCTCGAATGGCAAGCCAAAATTCCTTCCGGATAGAATA
TGATACCTTTGGTGAACTAAAGGTGCCAAATGATAAGTATTATGGCGCCCAGACCGTGAGATCTACGATGAACTTTAAGATTGGAGGTGTGACAGAACGC
ATGCCAACCCCAGTTATTAAAGCTTTTGGCATCTTGAAGCGAGCGGCCGCTGAAGTAAACCAGGATTATGGTCTTGATCCAAAGATTGCTAATGCAATAA
TGAAGGCAGCAGATGAGGTAGCTGAAGGTAAATTAAATGATCATTTTCCTCTCGTGGTATGGCAGACTGGATCAGGAACTCAGACAAATATGAATGTAAA
TGAAGTCATTAGCAATAGAGCAATTGAAATGTTAGGAGGTGAACTTGGCAGCAAGATACCTGTGCATCCCAACGATCATGTTAATAAAAGCCAGAGCTCA
AATGATACTTTTCCCACAGCAATGCACATTGCTGCTGCAATAGAAGTTCATGAAGTACTGTTACCAGGACTACAGAAGTTACATGATGCTCTTGATGCAA
AATCCAAAGAGTTTGCACAGATCATCAAGATTGGACGTACTCATACTCAGGATGCTGTTCCACTTACTCTTGGGCAGGAATTTAGTGGTTATGTTCAACA
AGTAAAATATGCAATGACAAGAATAAAAGCTGCCATGCCAAGAATCTATGAGCTCGCAGCTGGAGGCACTGCTGTTGGTACAGGTTTAAATACTAGAATT
GGCTTTGCAGAAAAGGTTGCTGCAAAAGTGGCTGCACTTACAGGCTTGCCTTTTGTCACTGCTCCGAATAAATTTGAAGCTCTGGCTGCTCATGACGCTC
TGGTTGAGCTCAGTGGAGCCATGAACACTACTGCCTGCAGTCTGATGAAGATAGCAAATGATATTCGATTTTTGGGTTCTGGTCCTCGGTCAGGTCTGGG
AGAATTGATCTTGCCTGAAAATGAACCAGGAAGCAGTATCATGCCAGGCAAGGTGAACCCTACTCAGTGTGAAGCAATGACCATGGTTGCAGCCCAAGTC
ATGGGGAACCATGTTGCTGTCACTGTCGGAGGCAGCAATGGACATTTTGAGTTGAATGTTTTCAAGCCAATGATGATTAAAAATGTGTTACACTCAGCCA
GGCTGCTGGGGGATGCTTCAGTTTCCTTTACAGAAAACTGCGTGGTGGGAATCCAGGCCAATACAGAAAGGATCAACAAGCTGATGAATGAGTCTCTAAT
GTTGGTGACAGCTCTCAATCCTCATATAGGGTATGACAAGGCAGCAAAGATTGCTAAGACAGCACACAAAAATGGATCAACCTTAAAGGAAACTGCTATC
GAACTTGGCTATCTCACAGCAGAGCAGTTTGACGAATGGGTAAAACCTAAGGACATGCTGGGTCCAAAGTGATTTACATAAATTTATAATGAAAATAAAC
ATGTATAAAATTTAAAAAAACAGACTCCCATTTCTTAAAAACGGATAAGTTTGAAAGGAAACTGCTATTGAACTTAAGCATCTCTAGCAGAGCAATTTGA
TCAGTATATAAAACCCTAGGATGTGCTAGGTCTAAGATGGATTAAACAAGTATAAAATAAAATACATTTATAAAATAAAAAGGAAAACAGACTTAAA

Loop counts:

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

Tetra-loop variants:

UGUU    1
UAAU    1
AAGU    1
GCAG    1
GCAC    1
CAAA    1
CUUA    1

Single bulge variants:

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

1 x 1 internal loop variants:

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