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

GTTTTTCCGGGAGAGACCACGCTTCCCCTCAAGCTCCCCAACGGCTCCGCCTTCCCGCCGGAGCCTGACCCTTCCCAGAGTGCCCGGCGATTCCGGCGTG
CGAGGCCCTTGGAGGGCAAGGCCCCAGGGCCTGGCTTAGGAGCGCGAGAGGCAGGCTGGGAATTGTAGTTCGAAGGCCCTCGAGAGCGGCTAGAGTCTGG
CGGCCGAGAGGACTAGTTGTCCCAGCGTGCCCTGCGCCTCAGCCCGCGCGCTCGCAGCTTCTCGCTCTCGCCTGCCTGCCCGCTCCCTTGCTTGCTCGCG
CTTTCGCTCGCCCTCTCCTCGAGGATCGAGGGGACTCTGACCACAGCCTGTGGCTGGGAAGGGAGACAGAGGCGGCGGCGGCTCAGGGGAAACGAGGCTG
CAGTGGTGGTAGTAGGAAGATGTCGGGCGAGGACGAGCAACAGGAGCAAACTATCGCTGAGGACCTGGTCGTGACCAAGTATAAGATGGGGGGCGACATC
GCCAACAGGGTACTTCGGTCCTTGGTGGAAGCATCTAGCTCAGGTGTGTCGGTACTGAGCCTGTGTGAGAAAGGTGATGCCATGATTATGGAAGAAACAG
GGAAAATCTTCAAGAAAGAAAAGGAAATGAAGAAAGGTATTGCTTTTCCCACCAGCATTTCGGTAAATAACTGTGTATGTCACTTCTCCCCTTTGAAGAG
CGACCAGGATTATATTCTCAAGGAAGGTGACTTGGTAAAAATTGACCTTGGGGTCCATGTGGATGGCTTCATCGCTAATGTAGCTCACACTTTTGTGGTT
GATGTAGCTCAGGGGACCCAAGTAACAGGGAGGAAAGCAGATGTTATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTACGCCTGGTCAAACCTGGAA
ATCAGAACACACAAGTGACAGAAGCCTGGAACAAAGTTGCCCACTCATTTAACTGCACGCCAATAGAAGGTATGCTGTCACACCAGTTGAAGCAGCATGT
CATCGATGGAGAAAAAACCATTATCCAGAATCCCACAGACCAGCAGAAGAAGGACCATGAAAAAGCTGAATTTGAGGTACATGAAGTATATGCTGTGGAT
GTTCTCGTCAGCTCAGGAGAGGGCAAGGCCAAGGATGCAGGACAGAGAACCACTATTTACAAACGAGACCCCTCTAAACAGTATGGACTGAAAATGAAAA
CTTCACGTGCCTTCTTCAGTGAGGTGGAAAGGCGTTTTGATGCCATGCCGTTTACTTTAAGAGCATTTGAAGATGAGAAGAAGGCTCGGATGGGTGTGGT
GGAGTGCGCCAAACATGAACTGCTGCAACCATTTAATGTTCTCTATGAGAAGGAGGGTGAATTTGTTGCCCAGTTTAAATTTACAGTTCTGCTCATGCCC
AATGGCCCCATGCGGATAACCAGTGGTCCCTTCGAGCCTGACCTCTACAAGTCTGAGATGGAGGTCCAGGATGCAGAGCTAAAGGCCCTCCTCCAGAGTT
CTGCAAGTCGAAAAACCCAGAAAAAGAAAAAAAAGAAGGCCTCCAAGACTGCAGAGAATGCCACCAGTGGGGAAACATTAGAAGAAAATGAAGCTGGGGA
CTGAGGTGGGTCCCATCTCCCCAGCTTGCTGCTCCTGCCTCATCCCCTTCCCACCAAACCCCAGACTCTGTGAAGTGCAGTTCTTCTCCACCTAGGACCG
CCAGCAGAGCGGGGGGATCTCCCTGCCCCCACCCCAGTTCCCCAACCCACTCCCTTCCAACAACAACCAGCTCCAACTGACTCTGGTCTTGGGAGGTGAG
GCTTCCCAACCACGGAAGACTACTTTAAATGAAAAAAAGAAATTGAATAATAAAATCAGGAGTCAAAATTCATCGTCTTCAAGCCCCTCTTTCTAGCCTT
TTCTACTACTCTCTGCTTGGTCAAGGTTTGTGCCCCACTACAGAACAGGGCTAAATTAGCCACCACCACTGAAAACTCAGCCGAATTTTTTTATACCACT
CTGATGTCAGCATTTTTTCCATCTGTTTGGGGCTTTTTCCTCTTTTTTCCATTCTCCCCAAATATTTTATCTGGCTTCAAAATTAAGAGGATTATTTTTC
AGATTGTTTTTATTCAGTGTGGCCGATTCCTCATCTGATTCAGGCTGTCCAGTCAGGCCCCTCCCATTTTAGGAGCTGGAGCCTTCATTTATGAAGAGAT
TCTCATCTATGAAATGGATCCTCATTTGTAAATCTTTTTTCTTCCATTTTCACAAAGCTGTAAAGAAATAATCCATCTCAACCTTACCCTTTTTCTCTGG
AGTCAGTGGGGTCTTTCCTCGCTCCATCTTACACAGACCTGAGCTGGAAGCTCAACTGGTTTTGTTCCCTGTTTGAAATATTGTGATCTCCCTCCCATGA
AAGAAAAACCAAGAACCAGAGGCGTAGACTGACTGAAGACACAACTCCTGGCTTTCTGAAGCTATGGACTTGGATTGGATTGCTGGGGGTTTGTAGAGAA
AGGTGACAAATTTCAGTACCTCTGGCATGCTGTCCCAGGAAACTAGGGCTCCCACTAACTTATGAGGTTTTTAAACA

Loop counts:

3 nts: 3
4 nts: 4
7 nts: 2
8 nts: 2
10 nts: 1

Tetra-loop variants:

AGUC    1
GAUC    1
UCUG    1
CUUU    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 1
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: 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