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

ATACCTAGCTCCAAGATCTTGGTTGCTAACACCATTCTCCAATAAAACGAACCAGGGATCGCTGGAGAAATAGCTGATTCTAAAACTAGGGCAGAAAGTA
TACAAGATGAGCCTGGAGCATCTTGTAGAGTCAGAGAGCAAGGCAGAACTTTATACATACAGTGATGTGAGATGGGCATGCAGAGGGAAGATGTTCCCAG
TGGCTGAAGCTGAAACAGTGTGAGCAACAAAATAAAGCAGTGTTGGATCACAACCCAAAGAATAAAATAAATATCCTCGAGCCCACACCGATATAAATAA
ATGATTGAATCAATAAATGAGTCCAGGCACTGTGGCTCATGCCTGTAATCCTGCACTTTGGGAGGCCAAGGCGGGTGGATCACTTGAGGTCAGGAGTTCG
AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGGTACATGCCTATAATCCCAGCTACTCAGGAGG
TGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAAATTGCAATGAGCCAAGATTGCAGGACTGCACTCCAGCCTAGGCGACAGAGTGAGACTCCATCTC
AAAAAAAAAAAAAAGGATGGACAAGACAAATCTCTTGTAAAAAAAATTACAAGTAATTTTTATAGAAGCTCTGCCCTGAGGGAGGGGGAGCGTGACTTCT
CACTCCTTCAGTGTGGGCTGCACAAGTGACTTCCTTCCATATGGGATCGTTATAACAAAAGACTGTAACAAGGGCTATGGGAGTTATAAGACAGGAATTG
TGGACAAAAACCAGTGTATATCATAACATCACACCTTGTAATGTTGGCAGTACAGTCACTGACCTTTGATAAATGTTGATGACATGTTGAGTAAAGGAAT
GAGAGAAAGAGGATTGTTTATCTCTGTTTTTATCCTTCTCAGAGAAACTTAGAGTAACAAGTGTGTTATCAGCCATGCTGATGCCTTTGGTAAACTATTG
TGTGAATATGGTTGTTTTGAATTGGTCAGTAGAAACTGGGCTGCCAGGCGCAGCCGGTAAGCATTTCCATGTGAGCCTTAGGGGAGAAGTGCATTTGGTA
GGAGCATCAAAATAGCTTCTGATATTTCATTAAAAGTTTGGGTCCGTCTGGTTCCTTCATTAGTATATGTCACTTCCTTTGACCTTCAGTGTCTGTTGAA
CCATGTGATTTTAGAAAGCAAGGGATTGCTTGACATCTCCAGGCTGTGAAGACTAAAGTTCACAGGAAAAGACTACAAGGAAATTTAAACAGTTTTATTA
TTTTCCCCCTCATTTCTTAATTTTCCTGCCACTACTCAGTACTGTGTGGGTCCAGGATCACCATTAGGGAAGACAGAGTAGCTCAGAAATCAGTAGTGAG
GAGGAGGACAGCACTTTGTGTGGTATCTTGCTCTAGGAGCATTTTCAAGCCATCAGAAGTGGGACTCTTGAAGACTATTTCTGACTTTCTCAGCACAAAT
TAAGATAATAGGAGATGGAGGCTCCATTTGAAAAACATTTTGGTTGTATAATGGTTAGCATAAAACATACTTTTTTCAAGTTAACTCAGGTACTAGAGTA
TGGGGGGCGGGGGGAAATGTACTGCAGCATTAATGAAAACTAGAGCTGGGAGAATGTGTTTTTCCTTGAGTAAATTGCAAATGCCTGTGCACCGCATTTG
ACCAGGAGGGAAGAATGAGAGGCCCTGGTAGCAAAGCCAGTGGAAGAAGTTTTACTAGGAGCAGTTGTATCATTCGTGTACTTTTTTTGTGTCATACAAG
TGAGAGTAAAATGGTCCATGTCTGTGTTTTGAGGAATTTTTTGCCTTTCTTTTCAGAAACTAATTCTGAAGCAAGCCCTTATAGTTGTGCTGCAGTGGTG
TTTCAATCACAATTTTAGTGTTCGACTGTATGCTTTAGTTGCTCTTAAGAAACTCTGGACTGTGTGTAAAGTGTTAAGTGTTGAAGAATTTGATGCCCTG
ACTCCTGTGATTGAATCCAGCCTCCATCAAGTGGAAAGCATGCACGGAGCAGGGAATGCCAAGAAGAATTGGCAACGCATTCAGGAGCATTTCTTTTTTG
CAACATTTCACCCACTCAAGGATTATTGTCTAGAGGCAGTGTCTGGCTTGTAAACAATGGAAGGGAATATTTAACTCTAAACAGAAATCTGTTCTGACAT
TAAAAGGAAATGAGTGAGAACATTTGTGCAGGTACTAATTTGGTCGAAGCAGATAACCAAGCGGAGTGGACCGACGTTCAGAAGAAGATTATCCCGTGGA
ACAGTCGTGTTTCCGACTTAGACCTGGAGCTCCTGTTTCAGGATCGTGCTGCCAGACTTGGAAAGTCAATTAGTAGACTCATCGTTGTGGCCTCGCTCAT
CGACAAACCGACCAATTTAGGAGGACCTGTGAGGTATTTGGGGCTTCAGTGCTCGTTGTTGGCAGCCTTCAGTGTATCAGCGACAAACAGTTTCAGCACC
TCAGTGTCTCTGCAGAACAGTGGCTTCCTCTAGTGGAGGTAAAACCACCTCAGCTAATTGATTATCTGCAGCAGAAGAAAACAGAAGGTTATACCATCAT
TGGAGTGGAACAAACTGCCAAAAGTTTAGACCTAACCCAATATTGCTTTCCTGAGAAATCTCTGCTCTTGTTGGGAAATGAACGTGAGGGAATTCCAGCA
AATCTGATCCAACAGTTGGACGTTTGTGTGGAAATTCCTCAACAGGGCATTATCCGCTCCCTGAATGTCCATGTGAGTGGAGCCCTGCTGATCTGGGAGT
ACACCAGGCAGCAGCTGCTCTCGCACGGAGATACCAAGCCATGATGTGCCTTCCTTAGTGAACTGCTGCTGCTGTTCAGACTTTTTTAAAAAAAACTATT
TGGACTAAAGAAACAGATTCTGAAATTTATTGTGATAATTTGTATTTCTTTTTTCTTGCAATTTAATGCCAAAAGTTTGCCATGTGCCTTAAACATATTA
CTATATATTTTCCCCTTTAATAAACACTTTTTGTTAAATTGTATTCTTCCTTTAATAAAATATTTTAAGCAATTGTGGAAAT

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: 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