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

AATCCTGCCGATCATGAGGTTTGCCGAGTGACCAATCTTCCCTCGTCTACAATTTGCTGGACTTGGAAAAGTGACTGGAAGGGAGCAGAGTTCCGTCAGC
CACTGCCAAGAAACCATTTAAATTACTAAGAGAGCGAAGGAAAGCACGTGACGTTCTGCAATCCCGTTGCAAGCGGTTTTGCAAGCCGGAGGTTGTTGCA
CCTTTTAGAGTCTAGGAAGCCCGCCTCTCGGTGGCGGAGTCGTCATTGGATGTTGCGGCTGTCAATCGCCAGGGCTATAAATAAGGGAGTCCGGCGGCTC
CTCTATCAGGAAGATTGTGCATGCCGTGGGTCTGACGGCTTGAGTAGCGCTAGGGAGAATCCCTGCAGGTAATATTTGACTTTTGCTTCATATTAATCTG
AGTGGAAAATAAAAGGGCCCTCTTCTCCTCTCGCTTCCCTGCCGGGCAGGCGCCATGGCGGAAGCCTCGGCGACGGGCGCCTGCGGAGAGGCGATGGCAG
CGGCGGAAGGCTCCTCGGGCCCGGCGGGCTTGACTCTGGGCCGGAGCTTCTCGAACTACCGGCCCTTCGAGCCCCAGGCGTTGGGCCTCAGCCCGAGCTG
GCGGCTGACGGGCTTCTCCGGCATGAAGGGCTGAGGCTGCAAGGTCCCGCAGGAGGCGCTGCTCAAACTCCTGGCGGGACTGACGCGGCCGGACGTGCGG
CCCCCGCTGGGCCGGGGCCTGGTGGGTGGCCAGGAAGAGGCGTCCCAGGAAGCCGGCCTGCCGGCAGGAGCGGGCCCCAGCCCCACCTTTCCAGCCCTGG
GCATCGGGATGGACTCCTGCGTCATCCCCCTGAGGCACGGGGGCCTGTCACTGGTGCAGACCACGGACTTCTTTTACCCCTTGGTAGAAGATCCCTACAT
GATGGGGCGCATAGCTTGTGCCAACGTGCTGAGTGACCTCTACGCCATGGGGATTACTGAGTGTGACAACATGTTGATGTTACTCAGCGTCAGCCAGAGT
ATGAGTGAGGAGGAACGCGAAAAGGTAACGCCACTCATGGTCAAAGGCTTTCGGGATGCGGCTGAGGAAGGAGGGACGGCAGTGACCGGTGGGCAAACGG
TGGTCAACCCTTGGATTATAATCGGTGGAGTTGCCACTGTAGTATGCCAACCAAATGAGTTCATAATGCCGGACAGCGCCGTCGTTGGGGACGTGCTGGT
GTTAACCAAACCGTTAGGAACCCAGGTTGCTGTCAATGCCCACCAATGGCTGGATAATCCTGAAAGATGGAATAAAGTAAAGATGGTGGTCTCCAGAGAA
GAGGTGGAGCTGGCCTATCAGGAAGCCATGTTCAATATGGCTACCCTCAACAGAACTGCTGCAGGTTTAATGCACACATTTAATGCCCATGCGGCCACAG
ATATCACAGGCTTTGGCATTCTAGGACACTCCCAGAACCTTGCAAAACAACAAAGAAATGAAGTGTCCTTTGTTATTCATAATCTGCCAATAATTGCCAA
GATGGCTGCCGTCAGCAAGGCCAGTGGACGGTTTGGGCTTCTTCAAGGAACCTCAGCTGAAACCTCTGGGGGATTACTGATTTGTCTGCCAAGAGAACAG
GCGGCTCGCTTTTGTTCTGAAATCAAATCCTCCAAGTACGGAGAGGGTCACCAAGCGTGGATCGTTGGCATTGTGGAAAAGGGAAACCGAACGGCCCGGA
TCATTGACAAGCCGCGAGTTATTGAAGTCCTGCCTCGTGGGGCCACAGCTGCTGTTCTTGCTCCTGACAGTTCAAATGCCTCCTCTGAGCCTAGCTCGTG
AGATGAAAGAACAGAAGTTGTTTGGACCTTAGAGCCATTGTCCACAATCACGGATGGTTCTCAAGAGTTGATTGTAAGAAATTTCCAAAGAAGGCTGCCT
GCATAGTGGTTCCGGCTGCCCTTTCTAGGTGATTGGAATCAGCCCATCTAAAGCAGTCTTTATATGCATTCCGAGGCCAGAGTAACATTTTGAACTTTGG
GGGGATATTTGTTCATCACTTGGGTAGAAGAGGAGCAAAAATACCTCTGTTTTCTCTTGCCAAAGTAAGATGAAGCTATTCCAGGTTGAGGGATTTTTCT
TTGCACGGGGTTGATTAATTTCTGCACAGGGAGTGAGATTATTAAAGTAACACACACACAAAGTAAATTGCAAAATGAAAAAAATTAGAAGCAAATGAGT
TTTGGACCAATATTGTTGATAAATCTAAATTGTTAAGAGAGATCTTATAATGCAACATCAAATTCTTTATTCAATTTTACTGAAGTACTGGCTCTTTCCT
GCTCTGGACAAGAATTGAGCAACTTGTCTGATGACTGGGAAAGGAGGACCTGCAACCATCTGACTTGGTCTCTGTTAATGACGTCTCTCCCTCTAAACCC
CATTAAGGACTGGGAGAGGCAGAGCAAGCCTCAGAGCCCAGGCCTCAGTGGTCATTAAGATGTTAAGTCTTTTGCGGCAGATTCCTGGTGATTTGATCAA
TAAAGAGTAATTTCTTGCTAAATAAATAAAAGAAACCTTGTTGAAAAACTA

Loop counts:

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

Tetra-loop variants:

GGAA    1
GCGA    1
GAUU    1
GAGA    1
CGGG    1
CCUU    1
GUUA    1

Single bulge variants:

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

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