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

AGCTTGCCCGGCATCACTCGCGGCATTGGAGTCAAGATGGAGGAGTACGCGCGAGAGCCTTGCCCATGGCGAATTGTGGATGACTGTGGTGGGGCCTTTA
CGATGGGTACCATTGGTGGTGGTATCTTTCAAGCAATCAAAGGTTTTCGCAATTCTCCAGTGGGAGTAAACCACAGACTACGAGGGAGTTTGACAGCTAT
TAAAACCAGGGCTCCACAGTTAGGAGGTAGCTTTGCAGTTTGGGGAGGGCTGTTTTCCATGATTGACTGTAGTATGGTTCAAGTCAGAGGAAAGGAAGAT
CCCTGGAACTCCATCACAAGTGGTGCCTTAACGGGAGCCATACTGGCAGCAAGAAATGGACCAGTGGCCATGGTTGGGTCAGCCGCAATGGGTGGCATTC
TCCTAGCTTTAATTGAAGGAGCTGGTATCTTGTTGACAAGATTTGCCTCTGCACAGTTTCCCAATGGTCCTCAGTTTGCAGAAGACCCCTCCCAGTTGCC
TTCAACTCAGTTACCTTCCTCACCTTTTGGAGACTATCGACAATATCAGTAGGACTTCTTTCCTAGGATTTCTTTAACAGAACGAGTTGTGGTTCGAGAA
GGATTTCAGAAGATCAAGTTACAGTCTGTTTTTAAAACCATAGGTGGGACAGCTATGGCCAATAGGCTATAAAGAGACATTTAGCACTTTTTTCTATTTA
AAGGAACAAGCGGGGAAGGGTGCTAAAAGATAATACGTTTATTTATTCACACTTGAATTGCATTTGTGATCAAAATAAATGTTTAAATCGCTAAAGGAAA
ATACAGTAAGTGCTTGAAAGATGAAGGACCAAAAGGCCAAAAAACAGTGAAATATGATCATCATCTCCTTGCGGACTTCTCTGCCTGGTTTTGTGTGTTC
TGTTATTCAAACAATAAAAAGCTGGTGGAACTTACTCTTTCTTTTAAGATAAGTTGTAGACTTCGATGTTTCATGCTCATGTACTTCAAATAATGCATGT
TTTATAGTTAGTCCCTCATCACTTGAAGTGACTTCTGAGAATTATGCAGAGTCAACATGGATCATTTCACAGTGAGATGCTTTATGGATTGAAGGATATG
GTAAAATGTTTATAGTTTACTTTGAAAGTAAAATATACTATGTCTTGGTTTTGAGGATATTGGATACAAAACTCTCTTCCTTTAGGGCTACTGAGTCTTG
ATTCCTGATCATCAGAAATTTCACCAGAAACAACTTGCTTCCAATATACCCAATTCTATATGAAGAATTCATGGAGAGTGTACTGGCACTGGAAGAGTTT
AGTGTTTCTTGTATGCTTGAAAATAAAGTATGTACTGTTTTGAATGTGTTCCAAGTCCTCTGCATAAACGATGTATTTTGGGGTCTGGTTGGGCCTGGAA
AATGGATGAGCACTTCAGAACAGGTCATTTTCCTGATATTGGAAGTGACATGTGGCCCTATAGGAGGCATGATGTTAGTTAATTACACATTTGCCTACAT
CTGTGGGAAATGGAGAACAAAGCCATGTGGGTACTGTAAACACACGTTTATCTTTTGGCCCAATGCCATACATATGGTAGGCATTTAATTACTGATTGTG
TTTGGATAATTTGGGAATTTTCGACTGTGGTAAAATATACATAAAATAATACTTATTAA

Loop counts:

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

Tetra-loop variants:

GCAU    1
UUGA    1
AAUA    1

Single bulge variants:

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