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

GAGTCGGGAAATGGCCGCTGTGTGGTTGCAACGGAGATAAATTCCCGGAACCGCGATTCGGCGTGTCAGGAATTCGAATTTAGAGTTTAATTTCTCAGAG
CATTCTCTCCAGGAAGAATTTTTACAGTATCTCAAAGACTTCACTTGACTTCTTGATCCTGCATAAAACCAAGGAGAAAAGAAATGGGTCGCTCCAATTC
TAGATCACATTCTTCAAGGTCAAAGTCTAGATCACAGTCTAGTTCTCGATCAAGATCAAGATCTCATTCTAGAAAGAAGCGATACAGTTCTAGGTCTCGT
TCCAGAACATATTCAAGGTCTCGTAGTAGAGATCGTATGTATTCTAGAGATTATCGTCGCGATTACAGAAATAATAGAGGAATGAGACGACCTTATGGGT
ACAGAGGAAGGGGTAGAGGGTATTATCAAGGAGGAGGAGGTAGATATCATCGAGGTGGTTATAGACCTGTCTGGAATAGAAGGCACTCTAGGAGTCCTAG
ACGAGGTCGTTCACGTTCCAGGAGTCCAAAAAGAAGATCCGTTTCTTCTCAAAGATCCAGAAGCAGATCTCGCCGGTCATATAGATCTTCTAGGTCTCCA
AGATCATCCTCTTCTCGTTCTTCATCCCCATATAGCAAATCTCCTGTTTCTAAAAGACGAGGGTCTCAGGAAAAACAAACCAAAAAAGCTGAAGGGGAAC
CCCAAGAAGAGAGTCCGTTGAAAAGTAAATCACAGGAGGAACCGAAAGATACATTTGAACATGACCCATCTGAGTCTATCGATGAATTTAATAAGTCATC
AGCCACATCCGGTGATATTTGGCCTGGCCTTTCAGCTTATGATAATAGTCCTAGATCACCCCATAGTCCTTCACCTATTGCTACACCACCTAGTCAGAGT
TCATCTTGCTCTGATGCTCCCATGCTCAGTACAGTTCACTCTGCAAAAAATACTCCTTCTCAGCATTCACATTCCATTCAGCATAGTCCTGAAAGGTCTG
GGTCTGGTTCTGTTGGAAATGGATCTAGTCGATACAGTCCTTCTCAGAATAGTCCAATTCATCACATCCCTTCACGAAGAAGTCCTGCAAAGACAATCGC
ACCACAGAATGCTCCAAGAGATGAGTCTAGGGGCCGTTCCTCGTTTTATCCTGATGGTGGAGATCAGGAAACTGCAAAGACTGGGAAGTTCTTAAAAAGT
CCCCCTCTACACAAGAATCTGGATGCACGAGAAAAGTCTACCTTCAGAGAGGAAAGCCCACTTAGGATCAAAATGATAGCGAGTGATTCTCACCGTCCTG
AAGTCAAACTCAAAATGGCACCTGTTCCTCTTGATGATTCTAACAGACCTGCTTCCTTGACTAAAGACAGGCTGCTTGCTAGTACACTTGTCCATTCTGT
CAAGAAGGAGCAAGAATTCCGATCCATCTTTGACCACATTAAGTTGCCACAGGCCAGCAAAAGCACTTCAGAGTCATTTATTCAACACATTGTGTCCTTG
GTTCATCATGTTAAAGAGCAATACTTCAAGTCAGCTGCAATGACCCTAAACGAGCGGTTCACTTCGTATCAGAAAGCCACTGAAGAACATAGTACTCGGC
AAAAGAGCCCTGAAATACACAGGAGAATTGACATCTCACCAAGTACCCTGAGGAAGCATACCCGTTTAGCAGGGGAAGAGAGAGTTTTTAAAGAAGAAAA
TCAAAAGGGAGATAAAAAATTAAGGTGTGACTCTGCTGACCTTCGGCATGACATTGATCGCCGTAGAAAAGAAAGAAGTAAAGAACGGGGAGATTCCAAG
GGCTCCAGGGAATCCAGTGGATCAAGAAAGCAGGAAAAAACTCCAAAAGATTACAAGGAATACAAATCTTACAAAGATGACAGTAAACATAAAAGAGAGC
AAGATCATTCTCGATCTTCATCCTCTTCAGCATCACCTTCTTCTCCCAGTTCTCGAGAAGAAAAGGAGAGTAAGAAGGAAAGAGAAGAAGAATTTAAAAC
TCACCATGAAATGAAAGAATACTCAGGCTTTGCAGGAGTTAGCCGACCACGAGGAACCTTTTTTCGAATTAGAGGCAGAGGAAGAGCCAGAGGAGTTTTT
GCTGGGACAAATACTGGTCCAAACAACTCAAATACTACTTTTCAAAAGAGACCGAAGGAAGAGGAATGGGATCCAGAATATACCCCAAAGAGCAAGAAGT
ACTTCTTGCATGACGACAGAGATGATGGTGTGGATTATTGGGCCAAAAGAGGAAGAGGTCGTGGTACTTTTCAACGTGGCAGAGGGCGCTTTAACTTCAA
AAAATCAGGTAGCAGTCCTAAATGGACTCATGACAAATACCAAGGGGATGGGATTGTTGAAGATGAAGAAGAGACCATGGAAAATAATGAAGAAAAGAAG
GACAGACGCAAGGAAGAAAAGGAATAATAAATATGAAGTAAGATTACAACAGAGCAGAACTTGCACCCACCATTTTTTTTACCTGATTTTTGTTTTCAAA
TAAGAATGTAAGCATTTTACTTAAATTTTACTGTTTGCAAGTAGTCTATAGAAATTTTGTTTTAAGTCTTCAAATATCTTGAGAAATAGTAGACTGTATG
TTGAAAATTGTACTGAAATAAAGTAGAAAATTGTTACGTACCATATTTGTAACTATCAACTTTTAAAACTTTTAACGTTTTTGTTACATGCATTGTAATT
CTGCTTTGTCTATAAGATATGGTCAAGTACAGCTCTGTGAAAGTTCTGATTCTCTTCCTTCCCTGTTTGTCAATGTTTTATTCTGAAGTAAACGTTAGCT
CTACATATAAATCCTGGAACAGAAATTGTTTATAGAGACTACACTAATTATTTTAACTGTATACATCTGTTTAATTTGAACACACTACATCGTAGGGTGA
CTGATTTTTGAAGTATACCACAGACAAAAAGTTGTTACTATGGTAAACTAAGCTAGTTTAACACTTGAGCAAATGCTTAAGAAGGAATTAAAAAAAAAAA
GCTTTGCCAATAGCTAAAAAGTACAAGCTATTAAAAATCAGATTGAAAAGTTTTGAGAAAATGTTATTTTTACTGAAAGCAAGCAGTGGCCTATAAAGAA
CATTCTTAGGAGCCTTTTCTATTTGCGTTCAAAACTGTGTGTTCTCTTTCTATTCCTATTTGATAGTTTGAGTCATGGTCTTAGATATTAGCTATTTGTG
AGAGGAAACTGGTTTGTAACAATACTGCAAATAGAAACCCCATTTCTACTGAACATCCTAGTTTTAAACAGAAGAAAAACTGTAATCCTGGGGTTGGTAT
GTAGGAGGTCTATCCTGCAGAATAAGTTGATACATTAGTACCTGATTTCATATCTTACATATTTATTTGAGCTGAACATTAGTTTGTAGTGTAACTATTA
GTAAAAATAGAGAAACACAGCATACTGTTCATTAATAGTATTTTAAAAAAATTGTTTTTCAAATGTCACCAATAAAAGTTTTGGCAGGAAGCTTGTTGCG
GCATTGATCTAACCTTTTTCCCCCCCATTTCAGTTGCAGTTTTTGTAGAATGGCTTTTTCTTTTTCCTCTTAAGAGTTCTATTCTTCAGGTAGATAATTT
TTCAAATGTGAATTATCTTTTGTGTCTATATTGATAGCTCTTAAAGGAGTGAAAATCTAAAATAGTAAATTTCAATGTTAAGTGTCTGCTTTATGGGCAT
ATATAAAAGTAGACACATTTCATTTGTTAATTTAGTTGTGTGTGTGTGTTAAAAGGAGCTAATGCTTATTCTGTTAATGTAAACTTTTGAAGATCTTAAG
TGTATTGCTCTTTCATCTTAAACACTTTCGAGGATTTGCAGTGCGTCTAGCACCTAGATTACAGCCAGGAACATTGGTTAAGAACTGTTGGAAACAAAAC
TAAAAGCAAACTCAACATATGTGATGTTTATGGCCCTCAGATCCTTAGTATTGTGTGATTTTCCCCCGTTAACATGTCTTTCTAAAATTGTCTATTAAAG
CAGAGGAAATACCTGCCAAAGGAAGTATGTATTGCATTAATCAGGGCATAACTAATATTCTCCTGTTCAGAATAATACTTATTTACGTGTGAAAGCAACA
TGGATGTGATTCCCAACACAGAATTTTCATGACCCTTTTATTGTATACAAATAAATACCATAACAGTTACTTGGTTAGACATCAAA

Loop counts:

5 nts: 1
8 nts: 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