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

CACACACACACACACACACACACACACCCCAACACACACACACACACCCCAACACACACACACACACACACACACACACACACACACACACACACACACA
CACACACAGCGGGATGGCCGAGCGCCGCACGCGTAGCACGCCGGGACTAGCTATCCAGCCTCCCAGCAGCCTCTGCGACGGGCGCGGTGCGTAAGTACCT
CGCCGGTGGTGGCCGTTCTCCGTAAGATGGCGGACCGGCGGCGGCAGCGCGCTTCGCAAGACACCGAGGACGAGGAATCTGGTGCTTCGGGCTCCGACAG
CGGCGGCTCCCCGTTGCGGGGAGGCGGGAGCTGCAGCGGTAGCGCCGGAGGCGGCGGCAGCGGCTCTCTGCCTTCACAGCGCGGAGGCCGAACCGGGGCC
CTTCATCTGCGGCGGGTGGAGAGCGGGGGCGCCAAGAGTGCTGAGGAGTCGGAGTGTGAGAGTGAAGATGGCATTGAAGGTGATGCTGTTCTCTCGGATT
ATGAAAGTGCAGAAGACTCGGAAGGTGAAGAAGGTGAATACAGTGAAGAGGAAAACTCCAAAGTGGAGCTGAAATCAGAAGCTAATGATGCTGTTAATTC
TTCAACAAAAGAAGAGAAGGGAGAAGAAAAGCCTGACACCAAAAGCACTGTGACTGGAGAGAGGCAAAGTGGGGACGGACAGGAGAGCACAGAGCCTGTG
GAGAACAAAGTGGGTAAAAAGGGCCCTAAGCATTTGGATGATGATGAAGATCGGAAGAATCCAGCATACATACCTCGGAAAGGGCTCTTCTTTGAGCATG
ATCTTCGAGGGCAAACTCAGGAGGAGGAAGTCAGACCCAAGGGGCGTCAGCGAAAGCTATGGAAGGATGAGGGTCGCTGGGAGCATGACAAGTTCCGGGA
AGATGAGCAGGCCCCAAAGTCCCGACAGGAGCTCATTGCTCTTTATGGTTATGACATTCGCTCAGCTCATAATCCTGATGACATCAAACCTCGAAGAATC
CGGAAACCCCGATATGGGAGTCCTCCACAAAGAGATCCAAACTGGAACGGTGAGCGGCTAAACAAGTCTCATCGCCACCAGGGTCTTGGGGGCACCCTAC
CACCAAGGACATTTATTAACAGGAATGCTGCAGGTACCGGCCGTATGTCTGCACCCAGGAATTATTCTCGATCTGGGGGCTTCAAGGAAGGTCGTGCTGG
TTTTAGGCCTGTGGAAGCTGGTGGGCAGCATGGTGGCCGGTCTGGTGAGACTGTTAAGCATGAGATTAGTTACCGGTCACGGCGCCTAGAGCAGACTTCT
GTGAGGGATCCATCTCCAGAAGCAGATGCTCCAGTGCTTGGCAGTCCTGAGAAGGAAGAGGCAGCCTCAGAGCCACCAGCTGCTGCTCCTGATGCTGCAC
CACCACCCCCTGATAGGCCCATTGAGAAGAAATCCTATTCCCGGGCAAGAAGAACTCGAACCAAAGTTGGAGATGCAGTCAAGCTTGCAGAGGAGGTGCC
CCCTCCTCCTGAAGGACTGATTCCAGCACCTCCAGTCCCAGAAACCACCCCAACTCCACCTACTAAGACTGGGACCTGGGAAGCTCCGGTGGATTCTAGT
ACAAGTGGACTTGAGCAAGATGTGGCACAACTAAATATAGCAGAACAGAATTGGAGTCCGGGGCAGCCTTCTTTCCTGCAACCACGGGAACTTCGAGGTA
TGCCCAACCATATACACATGGGAGCAGGACCTCCACCTCAGTTTAACCGGATGGAAGAAATGGGTGTCCAGGGTGGTCGAGCCAAACGCTATTCATCCCA
GCGGCAAAGACCTGTGCCAGAGCCCCCCGCCCCTCCAGTGCATATCAGTATCATGGAGGGACATTACTATGATCCACTGCAGTTCCAGGGACCAATCTAT
ACCCATGGTGACAGCCCTGCCCCGCTGCCTCCACAGGGCATGCTTGTGCAGCCAGGAATGAACCTTCCCCACCCAGGTTTACATCCCCACCAGACACCAG
CTCCTCTGCCCAATCCAGGCCTCTATCCCCCACCAGTGTCCATGTCTCCAGGACAGCCACCACCTCAGCAGTTGCTTGCTCCTACTTACTTTTCTGCTCC
AGGCGTCATGAACTTTGGTAATCCCAGTTACCCTTATGCTCCAGGGGCACTGCCTCCCCCACCACCGCCTCATCTGTATCCTAATACACAGGCCCCATCA
CAGGTATATGGAGGAGTGACCTACTATAACCCCGCCCAGCAGCAGGTGCAGCCAAAGCCCTCCCCACCCCGGAGGACTCCCCAGCCAGTCACCATCAAGC
CCCCTCCACCTGAGGTTGTAAGCAGGGGTTCCAGTTAATACAAGTTTCTGAATATTTTAAATCTTAACATCATATAAAAAGCAGCAGAGGTGAGAACTCA
GAAGAGAAATACAGCTGGCTATCTACTACCAGAAGGGCTTCAAAGATATAGGGTGTGGCTCCTACCAGCAAACAGCTGAAAGAGGAGGACCCCTGCCTTC
CTCTGAGGACAGGCTCTAGAGAGAGGGAGAAACAAGTGGACCTCGTCCCATCTTCACTCTTCACTTGAGTTGGCTGTGTTCGGGGGAGCAGAGAGAGCCA
GACAGCCCCAAGCTTCTGAGTCTAGATACAGAAGCCCATGTCTTCTGCTGTTCTTCACTTCTGGGAAATTGAAGTGTCTTCTGTTCCCAAGGAAGCTCCT
TCCTGTTTGTTTTGTTTTCTAAGATGTTCATTTTTAAAGCCTGGCTTCTTATCCTTAATATTATTTTAATTTTTTCTCTTTGTTTCTGTTTCTTGCTCTC
TCTCCCTGCCTTTAAATGAAACAAGTCTAGTCTTCTGGTTTTCTAGCCCCTCTGGATTCCCTTTTGACTCTTCCGTGCATCCCAGATAATGGAGAATGTA
TCAGCCAGCCTTCCCCACCAAGTCTAAAAAGACCTGGCCTTTCACTTTTAGTTGGCATTTGTTATCCTCTTGTATACTTGTATTCCCTTAACTCTAACCC
TGTGGAAGCATGGCTGTCTGCACAGAGGGTCCCATTGTGCAGAAAAGCTCAGAGTAGGTGGGTAGGAGCCCTTCTCTTTGACTTAGGTTTTTAGGAGTCT
GAGCATCCATCAATACCTGTACTATGATGGGCTTCTGTTCTCTGCTGAGGGCCAATACCCTACTGTGGGGAGAGATGGCACACCAGATGCTTTTGTGAGA
AAGGGATGGTGGAGTGAGAGCCTTTGCCTTTAGGGGTGTGTATTCACATAGTCCTCAGGGCTCAGTCTTTTGAGGTAAGTGGAATTAGAGGGCCTTGCTT
CTCTTCTTTCCATTCTTCTTGCTACACCCCTTTTCCAGTTGCTGTGGACCAATGCATCTCTTTAAAGGCAAATATTATCCAGCAAGCAGTCTACCCTGTC
CTTTGCAATTGCTCTTCTCCACGTCTTTCCTGCTACAAGTGTTTTAGATGTTACTACCTTATTTTCCCCGAATTCTATTTTTGTCCTTGCAGACAGAATA
TAAAAACTCCTGGGCTTAAGGCCTAAGGAAGCCAGTCACCTTCTGGGCAAGGGCTCCTATCTTTCCTCCCTATCCATGGCACTAAACCACTTCTCTGCTG
CCTCTGTGGAAGAGATTCCTATTACTGCAGTACATACGTCTGCCAGGGGTAACCTGGCCACTGTCCCTGTCCTTCTACAGAACCTGAGGGCAAAGATGGT
GGCTGTGTCTCTCCCCGGTAATGTCACTGTTTTTATTCCTTCCATCTAGCAGCTGGCCTAATCACTCTGAGTCACAGGTGTGGGATGGAGAGTGGGGAGA
GGCACTTAATCTGTAACCCCCAAGGAGGAAATAACTAAGAGATTCTTCTAGGGGTAGCTGGTGGTTGTGCCTTTTGTAGGCTGTTCCCTTTGCCTTAAAC
CTGAAGATGTCTCCTCAAGCCTGTGGGCAGCATGCCCAGATTCCCAGACCTTAAGACACTGTGAGAGTTGTCTCTGTTGGTCCACTGTGTTTAGTTGCAA
GGATTTTTCCATGTGTGGTGGTGTTTTTTGTTACTGTTTTAAAGGGTGCCCATTTGTGATCAGCATTGTGACTTGGAGATAATAAAATTTAGACTATAAA
CTTGGCTCCCTTGCCA

Loop counts:

4 nts: 1

Tetra-loop variants:

CCUU    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