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

AGGTTTGGGGTCAAGGAGCAAACTCTGCACAAGATGGCGGCGGTAGCGGCAGTGGCGGCGCGTAGGAGGCGGCTTTCTGTCTCTGGTCGTGATGAGAACA
GTGTGGAGTTAACCATGGCTGAGGGACCCTACAAGATCATCTTGACAGCACGGCCATTCCGCCTTGACCTACTAGAGGACCGAAGTCTTTTGCTTAGTGT
CAATGCCCGAGGACTCTTGGAGTTTGAGCATCAGAGGGCCCCTAGGGTCTCTTTCTCGGATAAGGTTAATCTCACGCTTGGTAGCATATGGGATAAGATC
AAGAACCTTTTCTCTAGGCAAGGATCAAAAGACCCAGCTGAGGGCGATGGGGCCCAGCCTGAGGAAACACCCAGGGATGGCGACAAGCCAGAGGAGACTC
AGGGGAAGGCAGAGAAAGATGAGCCAGGAGCCTGGGAGGAGACATTCAAAACTCACTCTGACAGCAAGCCGTATGGCCCCATGTCTGTGGGTTTGGACTT
CTCTCTGCCAGGCATGGAGCATGTCTATGGGATCCCTGAGCATGCAGACAACCTGAGGCTGAAGGTCACTGAGGGTGGGGAGCCATATCGCCTCTACAAT
TTGGATGTGTTCCAGTATGAGCTGTACAACCCAATGGCCTTGTATGGGTCTGTGCCTGTGCTCCTGGCACACAACCCTCATCGCGACTTGGGCATCTTCT
GGCTCAATGCTGCAGAGACCTGGGTTGATATATCTTCCAACACTGCCGGGAAGACCCTGTTTGGGAAGATGATGGACTACCTGCAGGGCTCTGGGGAGAC
CCCACAGACAGATGTTCGCTGGATGTCAGAGACTGGCATCATTGACGTCTTCCTGCTGCTGGGGCCCTCCATCTCTGATGTTTTCCGGCAATATGCTAGT
CTCACAGGAACCCAGGCGTTGCCCCCACTCTTCTCCCTCGGCTACCACCAGAGCCGTTGGAACTACCGGGACGAGGCTGATGTGCTGGAAGTGGATCAGG
GCTTTGATGATCACAACCTGCCCTGTGATGTCATCTGGCTAGACATTGAACATGCTGATGGCAAGCGGTATTTCACCTGGGACCCCAGTCGCTTCCCTCA
GCCCCGCACCATGCTTGAGCGCTTGGCTTCTAAGAGGCGGAAGCTGGTGGCCATCGTAGACCCCCACATCAAGGTGGACTCCGGCTACCGAGTTCACGAG
GAGCTGCGGAACCTGGGGCTGTATGTTAAAACCCGGGATGGCTCTGACTATGAGGGCTGGTGCTGGCCAGGCTCAGCTGGTTACCCTGACTTCACTAATC
CCACGATGAGGGCCTGGTGGGCTAACATGTTCAGCTATGACAATTATGAGGGCTCAGCTCCCAACCTCTTTGTCTGGAATGACATGAACGAACCATCTGT
GTTCAATGGTCCTGAGGTCACCATGCTCAAGGATGCCCAGCATTATGGGGGCTGGGAGCACCGGGATGTGCATAACATCTATGGCCTTTATGTGCACATG
GCGACTGCTGATGGGCTGAGACAGCGCTCTGGGGGCATGGAACGCCCCTTTGTCCTGGCCAGGGCCTTCTTCGCTGGCTCCCAGCGCTTTGGAGCCGTGT
GGACAGGGGACAACACTGCCGAGTGGGACCATTTGAAGATCTCTATTCCTATGTGTCTCAGCTTGGGGCTGGTGGGACTTTCCTTCTGTGGGGCGGATGT
GGGTGGCTTCTTCAAAAACCCAGAGCCAGAGCTGCTTGTGCGCTGGTACCAGATGGGTGCTTACCAGCCATTCTTCCGGGCACATGCCCACTTGGACACT
GGGCGACGAGAGCCATGGCTGTTACCATCTCAGCACAATGATATAATCCGAGATGCCTTGGGCCAGCGATATTCTTTGCTGCCCTTCTGGTACACCCTCT
TATATCAGGCCCATCGGGAAGGCATTCCTGTCATGAGGCCCCTGTGGGTGCAGTACCCTCAGGATGTGACTACCTTCAATATAGATGATCAGTACTTGCT
TGGGGATGCGTTGCTGGTTCACCCTGTATCAGACTCTGGAGCCCATGGTGTCCAGGTCTATCTGCCTGGCCAAGGGGAGGTGTGGTATGACATTCAAAGC
TACCAGAAGCATCATGGTCCCCAGACCCTGTACCTGCCTGTAACTCTAAGCAGTATCCCTGTGTTCCAGCGTGGAGGGACAATCGTGCCTCGATGGATGC
GAGTGCGGCGGTCTTCAGAATGTATGAAGGATGACCCCATCACTCTCTTTGTTGCACTTAGCCCTCAGGGTACAGCTCAAGGAGAGCTCTTTCTGGATGA
TGGGCACACGTTCAACTATCAGACTCGCCAAGAGTTCCTGCTGCGTCGATTCTCATTCTCTGGCAACACCCTTGTCTCCAGCTCAGCAGACCCTGAAGGA
CACTTTGAGACACCAATCTGGATTGAGCGGGTGGTGATAATAGGGGCTGGAAAGCCAGCAGCTGTGGTACTCCAGACAAAAGGATCTCCAGAAAGCCGCC
TGTCCTTCCAGCATGACCCTGAGACCTCTGTGTTGGTCCTGCGCAAGCCTGGCATCAATGTGGCATCTGATTGGAGTATTCACCTGCGATAACCCAAGGG
ATGTTCTGGGTTAGGGGGAGGGAAGG

Loop counts:

4 nts: 1
6 nts: 1

Tetra-loop variants:

AUGC    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: 0
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: 0