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

CCTCCCCTTCCCTACATCTAGCCGCCGCGCTTTCCCGCTCCCGCAGCAGCAGCCTCCCGCGTCGCTGTCGCTGTTGCCTCCGCCACCTCCTCCGCCGCCG
CGCGCCCCTCGGAGTTCCGCGCCCCACCATGCCCAACATCGTGCTGTTCAGCGGCAGCTCGCATCAGGACCTGTCCCAGCGCGTGGCCGACCGCCTGGGC
CTGGAGCTGGGCAAGGTGGTCACGAAGAAGTTCAGCAACCAGGAGACCAGCGTGGAGATTGGTGAAAGCGTGAGAGGGGAAGATGTCTACATCATCCAGA
GCGGCTGCGGGGAAATTAACGACAACCTGATGGAACTCCTCATCATGATCAATGCCTGCAAGATTGCGTCATCATCCAGAGTAACTGCCGTGATCCCGTG
TTTCCCATACGCCCGACAAGATAAAAAGGACAAGAGTCGTGCCCCAATTTCTGCAAAACTTGTGGCCAATATGCTGTCGGTGGCTGGGGCGGATCACATC
ATCACCATGGACCTGCATGCTTCTCAGATACAGGGATTCTTTGATATTCCTGTGGATAATTTGTATGCGGAGCCCGCAGTCCTGCAGTGGATTCGGGAAA
ACATTGCCGAGTGGAAGAACTGTATCATTGTTTCACCTGACGCAGGGGGAGCCAAAAGGGTTACATCAATTGCAGACAGGTTGAATGTGGAATTTGCTTT
GATCCACAAAGAGAGGAAGAAGGCGAATGAAGTGGACCGGATGGTCCTGGTGGGCGACGTGAAGGACCGTGTGGCCATCCTCGTGGATGACATGGCTGAC
ACTTGCGGCACCATCTGCCATGCTGCGGACAAGCTGCTGTCAGCTGGAGCCACCAAAGTGTATGCTATCCTTACCCATGGGATCTTCTCTGGACCAGCTA
TTTCCAGAATAAATAATGCCGCCTTTGAGGCTGTTGTCGTCACAAACACAATTCCGCAAGAGGACAAAATGAAACACTGCACCAAGATTCAGGTCATTGA
CATTTCCATGATCTTGGCCGAAGCAATCCGAAGGACACACAATGGGGAATCCGTGTCCTACCTGTTCAGCCATGTCCCGCTATAAATCCAGAATGGGAAG
TGTCCAGCAAGCCTACTCTGACTTCTGACTTGTTTTTGTTTTCTGGATTTTTAGCTGTAGGTATTCAGCAATGATAGGTTAATCACTGGCAAAAGCATCA
GATCTTTGTATATGCTAAGATTTATTGTTTCCCCTTCTAAAGCTCAAGATCATTTCTTTCCAGTTTTTGGGGAAATGGTGGTGGTTATTTGGTCTTTAAG
TGAACTGTCTTAAATGAGAAACGTTTTTGTCATTTTGACTTTTAACAGGTACAGGTGATCTCTTCCTTTGTTCTTTCAGTACTTTGAGGCGACAACTTTC
AAGTATATAATTTCATTGTGGAAGTCATAGTTTATATATTTCGAGGTTGCCAAAGGTGACTTCAGATTAAAGCCTTCTGTGTAAATATATACTGATAATG
CCTATGGACATTTGGGTAAAACCCTGTATAGAATTAATTATCCTTTTACTTTGGAGTGAACCTTGGAAAATTTATAATTATAATACCATGGATTTTGAAT
TTTCCTTTTTTTTTTTTTTTTGGATAACTCAGTTTCAGATAAACCATCTTGGTTACTGTGCTTAATTTGGACCAAATTTTATTTAGCTTAATATGGACAC
TGACACATTTTGGGGGGTATACATTAGACATATCAGAGCAGTGTATTTCTGGATCATTTTTTAAATGACCTCTTCTAAAACATAACTGTCACTTACCTGA
AATGCTGCATCCTAAAATTCCAAAATTATATTGAGCAATCGCCAAGGCCTAAAGCCAACTGACTTAAAGGTAATCATTTCAGCTAAGATTAAATTTAAAG
CCTAAGAATGTATAGAGCTAGTTTTAAAATAATGATCTCAGATTTTTAAAAAGGATATAGGAACCTGCATTGTCATTCTCTGAATTAAGAACTGATGGTT
TCTATCATTATTTAGCCCCACCTTTGTATTTTAAAATCCTTCAGAATACATTTATGAACCAATGCGACTGGACTTAGCCACACACAATGGAAATTCAGAC
CTTGACTATTTGGTGTTTCCAGTTCACAAAGGTGATGAAGACTGTCTTGGGAGCAGCTTAATCCCAAAATTTGTACATTTCTTGCTGCTCCTGGCGTGGA
AACTTAAGTGAGACCACCAAATACATTGGTCCTGTCCAATTCTACTGAATGGGGGTGGACCTGGCATTTATCTGGCCAAAAACAGGAGCCAGAGAAATAT
GAATATACCAAAGTTGTTTGTTTAGCCTCCAACTTAAATTACATTAGTCAACTTATAGATACTCATATGATCACTTTTCTTTTTAGATACTACATCAACT
AGATTCAGGAGTATATCATTTGCAGTGCTTGTATTGGTTTAAAATGTAAGATTTTAAGATCCTCTAACACTGTACTAAAACATTTCAATAAAATCATTCT
GACTGCGTTCA

Loop counts:

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

Tetra-loop variants:

UACU    2
AAAG    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: 1