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

AAATGTTTTCCGCATTAAGACGCTTCTTAGGAGTCTTCATGTAAGTTCATACACGACTTCCTTGTAGAATTGTGTCAATGAACATGCAATTAGGCTAGCT
GAACTTCAGGCCCTGAGAGTCTATGAAGCTAAAATAAGGCCCAGATGTGGGGTGGGAGGGGGAGTAGGCAGAGGCGGCAAAGGAGGACATTTCAGGCAAA
GGGAGCAGATGTCCAGGCAGGAAAGCACAAGGTAACGGGGGCACAGGGGGCGCACCACTTTTCCTGGAAGGAAAAAACAGCAGATGAGAGAAGGAGGTTG
GAGCCAGTTACCAGTAGAGGTCTATGTTCAAAGTCCAGAAGGAAGAAACAGCAGGACGGGGACAAAGAGAGGAAGGAGGAAAGGAGGCACGGTGTATGAA
ACTCTGTAGCCAAGAGCGCTAACAAATGAAAGGCAGGATGGGTGGAGGAAATGTACTGTGTTCCAAAGCTTCCTCTTATTTATGGGTGCTCCCGGGCCAC
AGAGGAGTAAACTGAAGGACTTCCCAGCTCCCCACTGCCCAGAGAGCTAGCGGAGTCCCGCCTCGCCCCGTCACATGGCCAGAGGCGCCCTCGGCACGTG
ACCTACCTCGCGCTAGGCCAATCAGCCTCTGCAGGGGCGGGGCCACCGAGTCCGCGGGGCGGGAGTCTCCGTCGGAGCCGCCTCTTCTCGCGATCCTTGC
GGCGGTCGCTCCTCAGCCGCCCACGACCCGGAGCGAAGGTCTCGCGAGGCCTGGGCGCTGCGGCGGCAGGAGGAGGACGGGGAAGGACGGAGCCGAGCCG
CGGCTGCCTCCCTCGCTCACTCCCTCGCGCACTCGCCCGCCCCCTCCCTCCCTCCCCTCCCTTCCCCGGCCCCGGCTCTGGCCCCGGCCCATTCGCTGTT
GGGTCTTCTGCTAGGGAGGATGTCGGGTTCGTCGCTGCCCAGCGCCCTGGCCCTCTCGCTGTTGCTGGTCTCTGGCTCCCTCCTCCCAGGGCCAGGCGCC
GCTCAGAACGAGCCAAGGATTGTCACCAGTGAAGAGGTCATTATTCGAGACAGCCCTGTTCTCCCTGTCACCCTGCAGTGTAACCTCACCTCCAGCTCTC
ACACCCTTACATACAGCTACTGGACAAAGAATGGGGTGGAACTGAGTGCCACTCGTAAGAATGCCAGCAACATGGAGTACAGGATCAATAAGCCGAGAGC
TGAGGATTCAGGCGAATACCACTGCGTATATCACTTTGTCAGCGCTCCTAAAGCAAACGCCACCATTGAAGTGAAAGCCGCTCCTGACATCACTGGCCAT
AAACGGAGTGAGAACAAGAATGAAGGGCAGGATGCCACTATGTATTGCAAGTCAGTTGGCTACCCCCACCCAGACTGGATATGGCGCAAGAAGGAGAACG
GGATGCCCATGGACATTGTCAATACCTCTGGCCGCTTCTTCATCATCAACAAGGAAAATTACACTGAGTTGAACATTGTGAACCTGCAGATCACGGAAGA
CCCTGGCGAGTATGAATGTAATGCCACCAACGCCATTGGCTCCGCCTCTGTTGTCACTGTCCTCAGGGTGCGGAGCCACCTGGCCCCACTCTGGCCTTTC
TTGGGAATTCTGGCTGAAATTATCATCCTTGTGGTGATCATTGTTGTGTATGAGAAGAGGAAGAGGCCAGATGAGGTTCCTGACGATGATGAACCAGCTG
GACCAATGAAAACCAACTCTACCAACAATCACAAAGATAAAAACTTGCGCCAGAGAAACACAAATTAAGTACTGCTTACAATATCTTTAGGTTCCTGAAA
CTGGTGGCAACATGACCTGCTAAAATTTTCTGCTTGGACCTCTTTGGTTCTCTCCCCTTTCAAGTGAGCAACACCACAATGACTGTCTAAAGCATGCCTT
ATTTAGCCTCTCCTGTAAGGGTGATCTAGCCAGGTACATTTTAAACAATGCTTCAGTGTAGAAGGTGTAAACTATTTTGGGCTTGATGTGCTGTGAATGT
TGCTTTTTTTTTTCCTTTGTTAAAATATTTAAATAGAAGTGAAAAGGTCCTCTGAGGATCAGATCATGCATGCGCCATTTTTTACTTAATGCAGCTGTTA
AATTGGCAAAGCTCTAAAATGCACTGCTGCCATCTAGTGATACACTTTTGTAAAGTACAGCAAAACCTACAGATATATACAGTATATAAATATATATATA
TATATATTTATATTTTTGGGGGTGGGAGAAATCCAAAATAAAGTAAATGCTTGTTTCATTTTTAAGCTGCTGATATTCATTCCTTATTGTATGTTGTCAG
ATGAGGAAATTGTGCAGTTCTGGTACATAAAGATGAGTAATATAAACTGAAATCTATAATTTTAAGGGCTTAACCTGTGACTTTAATAAGCTGGAACAGT
CCACTGAATGGGTATAATGAATTGCAGTATATACGTATGATTGCTTTTTAAGTGATTATCTTTTCTTCTGTTAAGTCATGTAAATTCATAAATCCTTTTG
CACTGATGTGTTGAACCTTATTCTTGTACATTCATTCAATCAAGGCAAACTTTTATAATTTTTCTTTTGTTTCCAATGACCTTGAAATGTTATAGCATGG
TAATATTCTATGCAACTATAGTTATACTTTTTGGTTTGACACTGTATTTTTTCACATTGATTTACTGGTTGATGATAGATTTTATAACCTAACGGTTCTC
ATGCGGTGCGTAATTGTAGATGCATGTACTTGTGTGTTTTGTGTAATTATTGAAGTGCAATGATGTATAAAAAAGTGGATTCACCTGTTTTTAAAAATAA
AACATTGATAAAAGGTG

Loop counts:

3 nts: 3
4 nts: 5
7 nts: 1
8 nts: 1

Tetra-loop variants:

AAAU    1
ACAG    1
UACU    1
UAAC    1
UAAU    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