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
GCCCCGCCGCCACCGCCGCGCCGAGTCCTTTTGTCCAAGATGGCGGCGCCGGGGGCGCTGCCTCCTCGGCCGCCGCCTCCGCCGCCGCCGCTGTGAGAAA
CCTACGGGCCGCCCGCCCGCCGCGCCAGCGCCATGAAGCGGCAGAGCGAGCGAGACTCTAGCCCGAGCGGGCGCGGCTCGTCATCGTCCGCCAAGCGTCC
GCGGGAGCGCGAACGGGAGGCGGAGGCGGGCGGGCGGCGGGCGGCGCACAAGGCCTCTGGCGGCGCCAAGCACCCGGTTCCAGCGCGGGCCCGCGACAAA
CCCCGCGGCAGCGGAAGCGGCGGGGGCGGGCATCGCGACGGCCGCGGCACCGGGGACGCGAATCACCGCGCGAGTAGCGGGCGCTCCTCGGGCTCCGGCG
CTGGCGGCGGGGGACGCGGCGGCAAGGCCTCGGGGGACCCGGGCGCCTCCGGCATGTCGCCCCGCGCGTCTCCTCTGCCGCCGCCTCCGCCACCGCCTGG
GGCCGAGCCCGCGTGTCCCGGCTCATCCGCGGCCGCGCCTGAGTACAAGACGTTGCTCATCAGCAGCTTGAGCCCCGCGCTGCCCGCCGAGCACCTCGAG
GACCGGCTCTTCCACCAGTTCAAGCGCTTCGGCGAGATCAGCCTCCGCCTGTCGCACACGCCTGAGCTGGGCCGTGTGGCCTACGTGAATTTCCGGCACC
CACAGGACGCACGCGAGGCCCGCCAGCACGCCCTGGCCCGGCAGCTGCTGCTCTACGACCGCCCGCTCAAGGTAGAGCCCGTGTACCTGCGTGGCGGCGG
CGGGAGCAGTCGGCGAAGTAGCAGCAGCAGCGCCGCCGCTTCCACGCCTCCCCCAGGGCCGCCCGCGCCCGCCGACCCGCTCGGCTACCTCCCGCTACAC
GGAGGCTACCAGTACAAGCAGCGCTCGCTGTCCCCCGTCGCTGCCCCGCCCCTGCGGGAGCCCCGTGCCCGTCACGCCGCCGCAGCCTTCGCCCTGGATG
CCGCTGCTGCCGCCGCCGTGGGACTGTCCCGGGAGCGGGCCCTGGACTACTACGGGCTGTACGACGACCGTGGGCGCCCCTATGGCTACCCAGCTGTGTG
TGAGGAGGACCTGATGCCCGAGGATGACCAGCGGGCCACGCGCAACCTCTTCATTGGTAACCTGGACCACAGCGTATCTGAGGTGGAGCTGCGAAGGGCC
TTCGAGAAATATGGCATCATCGAGGAGGTGGTCATCAAGAGGCCTGCCCGTGGCCAGGGCGGTGCCTATGCCTTCCTCAAGTTCCAGAACCTGGACATGG
CCCATAGGGCTAAGGTGGCCATGTCGGGCCGAGTGATTGGTCGCAACCCCATTAAGATAGGCTATGGCAAGGCCAACCCCACCACTCGTCTCTGGGTGGG
TGGCCTGGGACCTAACACGTCACTGGCGGCTCTGGCCCGAGAGTTTGACCGCTTTGGGAGCATTCGGACCATTGATCACGTCAAAGGAGATAGCTTTGCC
TATATTCAGTACGAGAGCTTGGACGCAGCCCAGGCCGCCTGTGCTAAAATGAGGGGTTTTCCCTTGGGTGGACCAGACCGCAGGCTCCGCGTGGATTTTG
CCAAAGCAGAGGAGACTCGGTACCCCCAGCAGTACCAGCCCTCGCCACTCCCTGTGCATTATGAGCTGCTCACAGATGGATACACCCGGCACCGCAACCT
GGACGCCGACCTGGTGCGGGACAGGACGCCCCCACACCTTCTGTACTCAGACCGAGACCGGACTTTTTTGGAAGGGGACTGGACCAGCCCCAGTAAAAGC
TCTGACCGCCGAAACAGCCTTGAGGGCTACAGTCGCTCAGTGCGCAGCCGGAGTGGTGAGCGTTGGGGGGCAGATGGAGACCGTGGTTTGCCCAAGCCCT
GGGAAGAGAGGCGGAAACGGAGAAGCCTTTCCAGTGACCGTGGGAGGACAACCCATTCACCATATGAGGAACGGAGTAGGACCAAGGGCAGTGGGCAGCA
GTCAGAGCGGGGCTCCGACCGCACCCCTGAGCGCAGCCGCAAGGAGAACCACTCCAGTGAAGGGACCAAGGAGTCCAGCAGCAACTCCCTCAGCAACAGC
AGACATGGGGCTGAGGAACGGGGCCACCACCACCACCACCACGAGGCTGCAGACTCTTCCCACGGGAAGAAGGCAAGAGACAGCGAGCGCAATCACCGGA
CCACAGAGGCCGAGCCCAAGCCTCTGGAAGAGCCAAAACACGAGACCAAAAAGCTGAAGAATCTTTCAGAGTACGCTCAGACACTACAGCTGGGTTGGAA
TGGGCTTCTGGTGTTGAAAAACAGCTGCTTCCCCACGTCTATGCATATCCTAGAGGGGGACCAGGGGGTGATCAGCAGTCTCCTCAAAGACCACACTTCT
GGGAGCAAGCTGACCCAGCTGAAGATCGCCCAGCGCCTTCGACTGGACCAGCCCAAGCTTGACGAGGTCACACGACGCATCAAGCAGGGGAGCCCCAACG
GCTATGCGGTCCTCTTAGCCACCCAGGCAACCCCCAGTGGGCTTGGCACTGAGGGGATGCCCACAGTAGAGCCCGGTCTGCAGAGGCGGCTTCTCAGGAA
CCTGGTCTCCTACTTGAAACAGAAGCAGGCCGCAGGGGTGATCAGCTTGCCAGTGGGGGGGTCCAAGGGCAGAGACGGCACAGGCATGCTCTACGCCTTC
CCACCCTGCGACTTTTCCCAGCAGTACCTCCAGTCAGCACTAAGGACATTGGGCAAGCTAGAAGAAGAACACATGGTGATAGTCATCGTCAGAGACACTG
CCTAGCCCAAGCCTGTCTTTCCCAGCGTCATGTTTGTGTCACAAAAGCAGTTATTTTAAAATCTGATCCCCTCTCTACCCTACCACTTTGGTTTGAATTA
TCTCCTGGGTTATTTTGGTTCATTTGGGTGGGGATCAAAGTCCTGTCCACCACCAAAACTAAGTTCTTAGATTTTGGGGGATTTTTTTTTTTAAACGATG
AGAAGGGAATCCGGTTATGTTGATTTCTAGTGTACAAGATACTGTCTGCTGTGGTTCTGTATTTTTTTATTTTTTGACCAACTGTATGGAAAGTTGTCAG
TAAAACCTTTGACAGAGGATGGATTTTTAAACCTGTTCAGAGTCCTGGTTTAATCAATCAAGCTAAAAGAATCGAAGACATCCCTAGTGCATGTACACGA
ATGCCCTACGTCATCCTTCCAGCACCACTGCTGCATGGGTCACTCTCGGCCTCTCAATTCTTCAGGCTCAGTCTGGACTCTACTTACACTCATTTTTATC
TTGGCTGACAGCAGGCAAGCTTCAGTTTGGGCTGTGGACGCTGCCACACAAGCCTGAGTAGAGCCCATGCAAAGGAAGGGATGGGGTGAGCGCAAGGCCT
GTGGTCAGCAGCTACTGATGGTTTTTTCTGCCTTAAACCGTGTGTGTGTCCATCATCATCAGTTTGAGCTGTGGCTGTTTGTTTGGGACAGAGTGCCCAC
TCAGCATGTTTGGCAGCAGGTAGCCTTCAGCAGCTGTGTAGTCTTGTACAAGGAGAAGCTGTGCACTGTTGATGCCAGGGGGTCTCGGGGCCCCTGATCT
GTCCAGGCTCCTGGTTCGGCCTACTTTCTAGCCTCACTCAGCCCAGGGATAGCCAGTGTTGGGAGACAGAGTTGCCTCAGGTTCCCAGGGGCCCGGGAGT
CCAAATACTGGAATGGAGGGTTGGAGGCAGCCTTCCTTGGATTTACTCATGAACTTTGCCTAGTTGTTTGTGATTTTTGGCTTTCTCTGGTCGTTCAGGG
GTGATGGGTAATAGAGCAGGCCCGTGTCCAGTCATACCTAGAGATTTGTGGGGGGATACTGAACCTCTAGACTGAAGTACTTACCGGGGAGCACAGTGGA
CTAGGGGATGCCCTTGATAATGACGGTTTCCTAGGTGCAAGATCAGAGCATGTGCCTACACCTTGTGCCCTGATGCCGAGGTGGAGACCATTGGGAAATA
ATTAATAGATATTTTTCTGGGGGGAAATCACAAGTCACTGAGGTGTTTGTTTGTTTGTTAGGCAGTGCTAGAGCTTGAAGCCACTCAAGCCAGTTGGGGA
GGAAAGGGATGCGGAGGTACCCTCTAGCTGGGAAGAAGGGTGAGATTCCGTCTTCTTCCCTGTCTCAAGTAAGTAAGGAAGGTACTGCGGACAGTGTGGG
CCAGGGAGGAAAACCAGAGCACACAGTTTTGTCACCATGGAACACCCCAAATGCCATTCTTCAGCGTGTCTGGTACCTTGGATGTTCAAACAGGGAACAC
TGTCAGGGCTGAGGAGAACAGAAGCTCTGGTAAGCGAATGAGCCCCTAGATGATAACCAGGAACTCCAGGTTCTGCTGGCCGTGGCATCCTCTCTCCAGG
TCTGCTCCCTTACCGGAGCTAGGATAAGGTAGCATGAGTGACACCTGAGATTAGAGGCTGGGGCTCACTGCAGGCTGTGGAGAGGTCATGCTGGTCCACA
GGAACACTTGGCAGTGCTCTCGTAGACCCCTCGGTGATGTGGAATGGACAGGTGCCTCGCAAGAGAGCAAGCACGTTCATAACAAAACAGCAACACAAAG
ACATGTTAAGCATGTTTATTTATTTGCCTGTTTTTGTTTTTTTACTTGAGCTGTGGTCACAGCTGCCAGGTACCTAAGCAAGTCAGTTGGGTACAGCAGG
ACACGCCACCATTCCAGGGTAGCTGGTACCGCCAGAAACAGGAGTGGGTCTTGTCCTGTTGCAGGCACACTGCAGTGGTTTTCCTGCAGCTCTCCAACAA
ACGCCTGAGTCACAGGCCAGAGCTGCCTTGGTATGTTGTTAAGTCCAAAACTTCTTCTCTGGGCTACCTATCTTCCTTCATGAAGCAGGTGCTCAGGACC
CGGAAGAATCATCTACCTCCCAGCTTTGTGAGACAGAACCAAGTAAAAGGAAACATGCTAGAAAACGTGCCTAGAGAAGACACTTCAACCTTTGCCTTAT
CCAACCCCTCTTCAGAGAAAGGTGTCCCATGGCCCCAAAAAGAACTGCCAAGTTTTGGTGAGGAGTAACACCCTGGCATGACATTCCTTCTCTTTCCTGG
CCCTCAACCACTTCCTTCCTTTGGCTCTTAAGACCTAGCAGGTTCTGTGAACTCTCAGGCCTTGGCCAGCACTAGTTAGGGGAGGTCAGGTGGTCAATGT
CCTGGTGATTTTATGAGACTGCCCCACTGAGAAAACTTACTTACTTCAGGCATCCAGTGCCCCCACCCAGGGTTCAGGCCCTGTCTAAGGTGTTGCTTAA
AGACAAAAAGGCAACATGTGCCTCACTGGTGGTGTGCCACTGTTCTCATGCTGCCTCCTAAGTGACTCCGATTTTCAGCCCTGGTAGAATAAGGAAGACA
GCTGATGCCTCCTTAGCCCCTTAGCACATGTTCCTAAGGTGTGTTGTCAAGCCAACCTGAATTCTGCCTCCCTGTTATAGTCCCTGTCTCCCCCACAGAG
ACCTGTGGGTGCTCCCAGCAGAGTTGAGACTGGCTCCGTTGAGTTAATGACTAGAATATAGTGCTTTCACTACTTGATTGTTAACCTGTTTTCTTCTGAT
GCCATCAGTACCAGCAGTCAGACTATTCCACTGGTTAAGTGTTTACTACCATTAAAGCGAGGCATGAAGCAAAGAGCTGAGTGAGTCCTCTGCTCTCCAG
AGGACCAAGAAATACCTGTGTGACACAGACCCACTTCAGTGTGTACAGCAAATTCTATAGTGCTTCTGAGCCCAGCAGGGCTTTACCTGCCCCTGGAGAG
TTTTAGCCGTCTTGTGTTTCTTGTTTACTTCACAACCAAATTTGTCCCCTCTTCTCTCTGTTAAGGGAGAGAAGTCACTTTAGCTGGATAATACCTATGT
AACAAACTGAGCAGCTGTTATTTGGGCAAAATCAAAGGAAGAAAGAGACTATGGTCTTCTATTTATTGTGGGAAGGAAAACAGGGTGGGGCGGGTGAGTG
AAAAGGTGGAAATCCCTGGTACCTTGCCTGGTGGTTACACAGTTTAACCATAGGCCAATTTTAGGGGCCTCTGAAGTATCTTTCTACAAACGCAGACAAG
CTCCACTACCCCTAACCTGCCAGGATGCTCAAGTCCACTGTCACAATCCCTTTCAGAAAACATTAGTGGCCGCTGCCCCAGCTACAGAGACGGCCGAAAT
GCTTTCACTCCTTAGCTTTGCCAACTCCATCCTCCAAAACTTCCCAGAATACCTCCCTTTCCAGTTCTACCAAATCTGTACTTGGGAGCAGCCTGCTGGA
TCCAGAACATGACAACAGAGAGCTGCGTCCACAGGGAACAAAGCCCTGACCTCTCTCTCCACATTACCCTTACAAAAACAGGCCCTCCCCATGAGAGAGC
TACACGGCAGGGGCAGACACTGTGAGTATAAGCTACTTTCCTCCCTGGAGTGCTCTATGTGGGCAGAACATGCTCTCCTTGCCTCTCCTGGAAGGTGTCT
TCTCTATGGCCTGGCTAGAGCTGCAAAAAAGGGACACACCCCACTTCGGTAAAAGAAAATAGGGAAAGGCCATAAACAAAGACAGACTTGTAGTTTATTT
TGTATTTTTTTTAAATAAATACACTTTACATTAAAGAAAAA

Loop counts:

3 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