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

GGCGCGCGCGCGGGAGCGAGCTTTGAAAGTTGAGCACGGCGGCGGCGAGCCGGTGCCCTGGGATCATGGTGGCGTTGCGGGGCCTTGGTAGCGGCCTGCA
GCCCTGGTGTCCGCTGGATCTTAGACTCGAATGGGTTGACACAGTGTGGGAACTGGATTTCACAGAGACTGAGCCTTTGGATCCCAGCATAGAAGCAGAG
ATCATAGAGACTGGATTGGCTGCATTCACAAAACTCTATGAAAGCCTTTTACCCTTTGCTACTGGAGAACATGGATCTATGGAGAGTATCTGGACCTTCT
TCATTGAGAACAATGTTTCCCATAGTACACTGGTGGCATTGTTCTATCATTTTGTTCAAATAGTTCATAAGAAGAATGTCAGTGTACAGTATCGAGAATA
TGGCCTTCATGCCGCTGGGCTTTACTTTTTGCTACTAGAAGTACCAGGCAGTGTAGCCAATCAAGTATTCCACCCAGTGATGTTTGACAAATGCATTCAG
ACTCTAAAGAAGAGCTGGCCCCAGGAATCTAACTTGAATCGGAAAAGAAAGAAAGAACAGCCTAAGAGCTCTCAGGCTAACCCCGGGAGGCATAGAAAAA
GGGGAAAGCCACCCAGGAGAGAAGATATTGAGATGGATGAAATTATAGAAGAACAAGAAGATGAGAATATTTGTTTTTCTGCCCGGGACCTTTCTCAAAT
TCGAAATGCCATCTTTCACCTTTTAAAGAATTTTTTAAGGCTTCTGCCAAAGTTTTCCTTGAAAGAAAAGCCACAATGTGTACAGAATTGTATAGAGGTC
TTTGTTTCATTAACTAATTTTGAGCCAGTTCTTCATGAATGTCATGTTACACAAGCCAGAGCTCTTAACCAAGCAAAATACATACCAGAACTGGCTTATT
ATGGATTGTATTTGCTGTGCTCTCCCATTCATGGAGAAGGAGATAAGGTCATCAGTTGTGTTTTCCATCAAATGCTCAGTGTAATATTAATGTTAGAAGT
TGGTGAAGGATCCCATCGTGCCCCCCTTGCTGTTACCTCCCAAGTCATCAACTGTAGAAACCAGGCGGTCCAGTTTATCAGCGCCCTTGTGGATGAATTA
AAGGAGAGTATATTCCCAGTCGTCCGTATCTTACTGCAGCACATCTGTGCCAAGGTGGTAGATAAATCAGAGTATCGTACTTTTGCAGCCCAGTCCCTAG
TCCAGCTGCTCAGTAAACTTCCTTGTGGGGAATACGCTATGTTCATTGCCTGGCTTTACAAATACTCCCGAAGTTCCAAGATCCCACACCGGGTTTTTAC
TCTTGATGTTGTCTTAGCTCTGTTAGAACTGCCTGAAAGAGAGGTGGATAACACCCTCTCCTTGGAGCATCAGAAGTTCTTAAAGCATAAGTTCCTGGTG
CAGGAAATTATGTTTGATCGTTGCTTAGACAAGGCGCCTACTGTCCGCAGCAAGGCACTGTCCAGCTTTGCACACTGTCTGGAGTTGACTGTTACCAGTG
CGTCGGAGAGTATCCTGGAGCTCCTGATTAACAGTCCTACGTTTTCTGTAATAGAGAGTCACCCTGGTACCTTACTGAGAAATTCATCAGCTTTTTCCTA
CCAAAGGCAGACATCTAACCGTTCCGAACCCTCAGGGGAGATCAACATAGACAGCAGTGGTGAAACAGTTGGATCTGGAGAAAGATGTGTCATGGCAATG
CTGAGAAGGAGGATCAGGGATGAGAAGACCAACGTTAGGAAGTCTGCACTGCAGGTATTAGTGAGTATTTTGAAACACTGTGATGTCTCAGGCATGAAGG
AAGACCTGTGGATTCTGCAGGACCAGTGTCGGGACCCTGCAGTGTCTGTCCGGAAGCAGGCCCTCCAGTCTCTTACTGAACTCCTTATGGCTCAGCCTAG
ATGCGTGCAGATCCAGAAAGCCTGGTTGCGGGGGGTGGTCCCGGTGGTGATGGACTGCGAGAGCACTGTGCAGGAGAAGGCCCTGGAGTTCCTGGACCAG
CTGCTGCTGCAGAACATCCGGCATCACAGTCATTTTCACTCTGGGGACGACAGCCAGGTCCTCGCCTGGGCGCTTCTTACTCTCCTCACCACCGAAAGCC
AGGAACTGAGCCGATATTTAAATAAGGCTTTTCATATCTGGTCCAAGAAAGAAAAATTCTCACCCACTTTTATAAACAATGTAATATCTCACACTGGCAC
GGAACATTCGGCACCTGCCTGGATGCTGCTCTCCAAGATTGCTGGCTCCTCACCCAGGCTGGACTACAGCAGAATAATACAATCTTGGGAGAAAATCAGC
AGTCAGCAGAATCCCAATTCAAACACCTTAGGACATATTCTCTGTGTGATTGGGCATATTGCAAAGCATCTTCCTAAGAGCACCCGGGACAAAGTGACTG
ATGCTGTCAAGTGTAAGCTGAATGGATTTCAGTGGTCTCTAGAGGTGATCAGTTCAGCTGTTGACGCCTTGCAGAGGCTTTGTAGAGCATCTGCAGAGAC
ACCAGCAGAGGAGCAGGAATTGCTGACGCAGGTGTGTGGGGATGTACTCTCCACCTGCGAGCACCGCCTCTCCAACATCGTTCTCAAGGAGAATGGAACA
GGGAATATGGACGAAGACCTGTTGGTGAAGTACATTTTTACCTTAGGGGATATAGCCCAGCTGTGTCCAGCCAGGGTGGAGAAGCGCATCTTCCTTCTGA
TTCAGTCCGTCCTGGCTTCGTCTGCTGATGCTGACCACTCACCATCATCTCAAGGCAGCAGTGAGGCCCCAGCGTCTCAGCCACCCCCCCAGGTCAGAGG
TTCTGTCATGCCCTCTGTGATTAGAGCACATGCCATCATTACCTTAGGTAAGCTGTGCTTACAGCACGAGGATCTGGCAAAGAAGAGCATCCCAGCCCTG
GTGCGAGAGCTCGAGGTGTGTGAGGACGTGGCTGTCCGCAACAACGTCATCATTGTAATGTGCGATCTCTGCATTCGCTACACCATCATGGTGGACAAGT
ATATTCCCAACATCTCCATGTGTCTGAAGGATTCCGACCCATTCATCCGGAAGCAGACACTCATCTTGCTTACCAATCTCTTGCAGGAGGAATTTGTGAA
ATGGAAGGGCTCCCTGTTCTTCCGATTTGTCAGCACTCTGATCGATTCACACCCAGACATTGCCAGCTTCGGGGAGTTTTGCCTGGCTCACCTGTTACTG
AAGAGGAACCCTGTCATGTTCTTCCAACACTTCATTGAATGTATTTTTCACTTTAATAACTATGAGAAGCATGAGAAGTACAACAAGTTCCCCCAGTCAG
AGAGAGAGAAGCGGCTGTTTTCATTGAAGGGAAAGTCAAACAAAGAGAGACGAATGAAAATCTACAAATTTCTTCTAGAGCACTTCACAGATGAACAGCG
ATTCAACATCACTTCCAAAATCTGCCTTAGTATTTTGGCGTGCTTTGCTGATGGCATCCTACCCCTGGACCTGGACGCCAGTGAGTTACTCTCAGACACG
TTTGAGGTCCTCAGCTCAAAGGAGATCAAGCTTTTGGCAATGAGATCTAAACCAGACAAAGACCTCCTTATGGAAGAAGATGACATGGCCTTGGCAAATG
TAGTCATGCAGGAAGCTCAGAAGAAGCTCATCTCACAAGTTCAGAAGAGGAATTTCATAGAAAATATTATTCCAATTATCATCTCCCTGAAGACTGTGCT
GGAGAAAAATAAGATCCCAGCTTTGCGGGAACTCATGCACTATCTCAGGGAGGTGATGCAGGATTACCGAGATGAGCTCAAGGACTTCTTTGCAGTTGAC
AAACAGCTGGCATCAGAGCTTGAGTATGACATGAAGAAGTACCAGGAACAGCTGGTCCAGGAGCAGGAGCTAGCAAAACATGCAGATGTGGCCGGGACGG
CTGGAGGTGCTGAGGTGGCACCTGTGGCACAGGTTGCCCTGTGTTTAGAAACAGTGCCAGTTCCTGCTGGCCAAGAAAACCCTGCCATGTCACCTGCCGT
GAGCCAGCCCTGCACACCCAGGGCAAGTGCTGGCCATGTAGCAGTATCATCTCCTACACCTGAAACAGGGCCATTGCAGAGGTTGCTGCCCAAAGCCAGG
CCCATGTCCCTGAGCACCATTGCAATCCTGAATTCTGTCAAGAAAGCCGTGGAGTCAAAGAGCAGGCATCGGAGTCGGAGCTTAGGAGTGCTGCCTTTCA
CTTTAAATTCTGGAAGCCCAGAAAAAACGTGCAGTCAGGTGTCTTCATACAGTTTGGAGCAAGAGTCGAATGGCGAGATTGAGCACGTGACCAAGCGGGC
CATCAGCACCCCCGAGAAGAGCATCAGTGATGTCACGTTTGGAGCAGGGGTCAGTTACATCGGGACACCACGGACTCCGTCGTCAGCCAAAGAGAAAATT
GAAGGCCGGAGTCAAGGAAATGACATCTTATGTTTATCACTGCCTGATAAACCGCCCCCACAGCCTCAGCAGTGGAATGTGCGGTCTCCCGCCAGGAATA
AAGACACTCCAGCCTGCAGCAGGAGGTCCCTCCGAAAGACCCCTCTGAAAACAGCCAACTAAACAGCGCCTCCCACCAGTGTCCAGGCAGGCAGGAGCCC
TTGAGGAAGCAGTCTCGTGTCCTCCGTGTGAAGGCAGCTGGATCACTTCCCGCAGTCCTTGGGCAGCGCTTTGCTGTGGAACACGAGAGCTCCTCCTCAG
GGGCCTGGCACTCACCTTCTATTCTGTATGATGTATTTGGTTAAACACTGTCAAATAATAGAGATGTGCCAGATTTAGATTTTCTTACCCTAATCTGTTT
AATATTGTAACTTTATTCCATTTGAAAGTGTCAAGCCCATTCAGATAAGCTATAATCTGGTCTTTAAGGAACACAACTTTAAAACTGCAGCTTTCTTTTA
TATAAATCAAGCCTCTGTTAACTTGAATTCCTTATAGTACATATTTTCCCATCTGTAATGACGAAATTTTGATTCTAATATTTTTTCTATTATTTATAAG
TGCAAATTTTTTAAAAAAGTGTACAGCTTTCTAAAAGTAATAAAGGTTTAGCATAAATACA

Loop counts:

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

Tetra-loop variants:

AUUC    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 0
U x 0 bulge: 1
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: 1
U x C bulge: 1
C x G bulge: 0
C x A bulge: 0
C x U bulge: 1
C x C bulge: 0