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

AAGTGGGCGGGGGAAGGCGCGAGAGCGAGCGCGAGAGGGAAAAGGAGGGAGGGGGTGGGGAAGAGGGAATCTTATATCACGTGACAGGGGCGGCGCGGCC
CGGGGTGTCAGTGTGGAGGAGACTGAGTATTCTACCTTGTAAATACTGTTATTTGTATATACTGTAAATGATGACATCGGTGGGCACTAACCGAGCCCGG
GGAAACTGGGAACAACCTCAAAACCAAAACCAGACACAGCACAAGCAGCGGCCACAGGCCACTGCAGAACAAATTAGACTTGCACAGATGATTTCGGACC
ATAATGATGCTGACTTTGAGGAGAAGGTGAAACAATTGATTGATATTACAGGCAAGAACCAGGATGAATGTGTGATTGCTTTGCATGACTGCAATGGAGA
TGTCAACAGAGCTATCAATGTTCTTCTGGAAGGAAACCCAGACACGCATTCCTGGGAGATGGTCGGGAAGAAGAAGGGAGTCTCAGGCCAGAAGGATGGT
GGCCAGACGGAATCCAATGAGGAAGGCAAAGAAAATCGAGACCGGGACAGAGACTATAGTCGGCGACGTGGTGGGCCACCAAGACGGGGGAGAGTTCGAG
GTCAGGAAAATGGATTGGATGGCACCAAGAGTGGAGGGCCTTCTGGAAGAGGAACAGAAAGAGGCAGAAGGGGCCGTGGCCGAGGCAGAGGTGGCTCTGG
TAGGCGAGGAGGAAGGTTTTCTGCTCAAGGAATGGGAACCTTTAACCCAGCTGATTATGCAGAGCCAGCCAATACTGATGATAACTATGGCAATAGCAGC
GGCAATACGTGGAACAACACTGGCCACTTTGAACCAGATGATGGGACGAGTGCATGGAGGACTGCAACAGAGGAGTGGGGGACTGAAGATTGGAATGAAG
ATCTTTCTGAGACCAAGATCTTCACTGCCTCTAATGTGTCTTCAGTGCCTCTGCCTGCGGAGAATGTGACAATCACTGCTGGTCAGAGAATTGACCTTGC
TGTTCTGCTGGGGAAGACACCATCTACAATGGAGAATGATTCATCTAATCTGGATCCGTCTCAGGCTCCTTCTCTGGCCCAGCCTCTGGTGTTCAGTAAT
TCGAAGCAGACTGCCATATCACAGCCTGCTTCAGGGAACACATTTTCTCATCACAGTATGGTGAGCATGTTAGGGAAAGGATTTGGTGATGTCGGTGAAG
CTAAAGGCGGCAGTACTACAGGCTCCCAGTTCTTGGAGCAATTCAAGACTGCCCAAGCCCTGGCTCAGTTGGCAGCTCAGCATTCTCAGTCTGGAAGCAC
CACCACCTCCTCTTGGGACATGGGCTCGACGACACAATCCCCATCACTGGTGCAGTATGATTTGAAGAACCCAAGTGATTCAGCAGTGCACAGCCCCTTT
ACAAAGCGCCAGGCTTTTACCCCATCTTCAACCATGATGGAGGTGTTCCTTCAGGAGAAGTCACCTGCAGTGGCTACCTCCACAGCTGCACCTCCACCTC
CGTCTTCTCCTCTGCCAAGCAAATCCACATCGGCTCCACAGATGTCGCCTGGATCTTCAGACAACCAGTCCTCTAGCCCTCAGCCGGCTCAGCAGAAACT
GAAACAGCAGAAGAAAAAAGCCTCCTTGACTTCTAAGATTCCTGCTCTGGCTGTGGAGATGCCTGGCTCAGCAGATATCTCAGGGCTAAACCTGCAGTTT
GGGGCATTGCAGTTTGGGTCAGAGCCTGTCCTTTCTGATTATGAGTCCACCCCCACCACGAGCGCCTCTTCAAGCCAGGCTCCAAGTAGCCTGTATACCA
GCACGGCCAGTGAATCATCCTCTACAATTTCATCTAACCAGAGTCAGGAGTCTGGTTATCAGAGCGGCCCAATTCAGTCGACAACCTATACCTCCCAAAA
TAATGCTCAGGGCCCTCTTTATGAACAGAGATCCACACAGACTCGGCGGTACCCCAGCTCCATCTCTTCATCACCCCAAAAGGACCTGACTCAGGCAAAG
AATGGCTTCAGTTCTGTGCAGGCCACGCAGTTACAGACCACACAATCTGTTGAAGGTGCTACAGGCTCTGCAGTGAAATCTGATTCACCTTCCACTTCTA
GCATCCCCCCTCTCAATGAAACGGTATCTGCAGCTTCCTTACTGACGACAACCAATCAGCATTCATCCTCCTTGGGTGGCTTGAGCCACAGTGAGGAGAT
TCCAAATACTACCACCACACAACACAGCAGCACGTTATCTACGCAGCAGAATACCCTTTCATCATCAACATCTTCTGGGCGCACTTCGACATCCACTCTT
TTGCACACAAGTGTGGAGAGTGAGGCGAATCTCCATTCTTCCTCCAGCACTTTTTCCACCACATCCAGCACAGTCTCTGCACCTCCCCCAGTGGTCAGTG
TCTCCTCCAGTCTCAATAGTGGCAGTAGCCTGGGCCTCAGCCTAGGCAGCAACTCCACTGTCACAGCCTCGACTCGAAGCTCAGTTGCTACGACTTCAGG
AAAAGCTCCTCCCAACCTCCCTCCTGGGGTCCCGCCGTTGTTGCCTAATCCGTATATTATGGCTCCAGGGCTGTTACATGCCTACCCGCCACAAGTATAT
GGTTATGATGACTTGCAGATGCTTCAGACAAGATTTCCATTGGATTACTACAGCATCCCATTTCCCACACCCACTACTCCGCTGACTGGGAGGGATGGTA
GCCTGGCCAGCAACCCTTATTCTGGTGACCTCACAAAGTTCGGCCGTGGGGATGCCTCCTCCCCAGCCCCGGCCACAACCTTGGCCCAACCCCAACAGAA
CCAGACGCAGACTCACCATACCACGCAGCAGACATTCCTGAACCCGGCGCTGCCTCCTGGCTACAGTTACACCAGCCTGCCATACTATACAGGGGTCCCG
GGCCTCCCCAGCACCTTCCAGTATGGGCCTGCTGTGTTCCCTGTGGCTCCTACCTCTTCCAAGCAGCATGGTGTGAATGTCAGTGTGAATGCATCGGCCA
CCCCTTTCCAACAGCCGAGTGGATATGGGTCTCATGGATACAACACTGGAAGAAAATATCCACCCCCTTACAAGCATTTCTGGACGGCTGAGAGCTAATT
TGGCCCAAGGCTGGGGGCTGTGTTTTGTGTGTGTGTATAAATTTGCACTGAAGTCTTGTTTCAGAAACCAGACCACTGAGGAGAGCCTGCTGAGCTGAGG
CCATGGCCTGCGTGGCTTGGGGAAATGAGTTGGTGGATACCTTCTGGGCTTTTGAACTTGCCCCTCCCCCATTTCCCTCTCCCCCATGTGTCTGACCCTG
TCTTACCCATTTCAAGTTCAAGCGGTGCAGCACCTTCGAAGCATCAATGCACACACCTGCTGTTGCTTTTGATTTCTGGAAGGCATGTAGTTTCAACTTG
TAACAAAAATATTTGTAGTCTTCAATAAACTGTGGTATTTCTTTAGCTAAC

Loop counts:

5 nts: 1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 0
U x 0 bulge: 0
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