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

CAGCAACTATGAAATAATCGTAGTATGAGAGGCAGAGATCGGGGCGAGACAATGGGGATGTGGGCGCGGGAGCCCCGTTCCGGCTTAGCAGCACCTCCCA
GCCCCGCAGAATAAAACCGATCGCGCCCCCTCCGCGCGCGCCCTCCCCCGAGTGCGGAGCGGGAGGAGGCGGCGGCGGCCGAGGAGGAGGAGGAGGAGGC
CCCGGAGGAGGAGGCGTTGGAGGTCGAGGCGGAGGCGGAGGAGGAGGAGGCCGAGGCGCCGGAGGAGGCCGAGGCGCCGGAGCAGGAGGAGGCCGGCCGG
AGGCGGCATGAGACGAGCGTGGCGGCCGCGGCTGCTCGGGGCCGCGCTGGTTGCCCATTGACAGCGGCGTCTGCAGCTCGCTTCAAGATGGCCGCTTGGC
TCGCATTCATTTTCTGCTGAACGACTTTTAACTTTCATTGTCTTTTCCGCCCGCTTCGATCGCCTCGCGCCGGCTGCTCTTTCCGGGATTTTTTATCAAG
CAGAAATGCATCGAACAACGAGAATCAAGATCACTGAGCTAAATCCCCACCTGATGTGTGTGCTTTGTGGAGGGTACTTCATTGATGCCACAACCATAAT
AGAATGTCTACATTCCTTCTGTAAAACGTGTATTGTTCGTTACCTGGAGACCAGCAAGTATTGTCCTATTTGTGATGTCCAAGTTCACAAGACCAGACCA
CTACTGAATATAAGGTCAGATAAAACTCTCCAAGATATTGTATACAAATTAGTTCCAGGGCTTTTCAAAAATGAAATGAAGAGAAGAAGGGATTTTTATG
CAGCTCATCCTTCTGCTGATGCTGCCAATGGCTCTAATGAAGATAGAGGAGAGGTTGCAGATGAAGATAAGAGAATTATAACTGATGATGAGATAATAAG
CTTATCCATTGAATTCTTTGACCAGAACAGATTGGATCGGAAAGTAAACAAAGACAAAGAGAAATCTAAGGAGGAGGTGAATGATAAAAGATACTTACGA
TGCCCAGCAGCAATGACTGTGATGCACTTAAGAAAGTTTCTCAGAAGTAAAATGGACATACCTAATACTTTCCAGATTGATGTCATGTATGAGGAGGAAC
CTTTAAAGGATTATTATACACTAATGGATATTGCCTACATTTATACCTGGAGAAGGAATGGTCCACTTCCATTGAAATACAGAGTTCGACCTACTTGTAA
AAGAATGAAGATCAGTCACCAGAGAGATGGACTGACAAATGCTGGAGAACTGGAAAGTGACTCTGGGAGTGACAAGGCCAACAGCCCAGCAGGAGGTATT
CCCTCCACCTCTTCTTGTTTGCCTAGCCCCAGTACTCCAGTGCAGTCTCCTCATCCACAGTTTCCTCACATTTCCAGTACTATGAATGGAACCAGCAACA
GCCCCAGCGGTAACCACCAATCTTCTTTTGCCAATAGACCTCGAAAATCATCAGTAAATGGGTCATCAGCAACTTCTTCTGGTTGATACCTGAGACTGTT
AAGGAAAAAAATTTTAAACCCCTGATTTATATAGATATCTTCATGCCATTACAGCTTTCTAGATGCTAATACATGTGACTATCGTCCAATTTGCTTTCTT
TTGTAGTGACATTAAATTTGGCTATAAAAGATGGACTACATGTGATACTCCTATGGACGTTAATTGAAAAGAAAGATTGTTGTTATAAAGAATTGGTTTC
TTGGAAAGCAGGCAAGACTTTTTCTCTGTGTTAGGAAAGATGGGAAATGGTTTCTGTAACCATTGTTTGGATTTGGAAGTACTCTGCAGTGGACATAAGC
ATTGGGCCATAGTTTGTTAATCTCAACTAACGCCTACATTACATTCTCCTTGATCGTTCTTGTTATTACGCTGTTTTGTGAACCTGTAGAAAACAAGTGC
TTTTTATCTTGAAATTCAACCAACGGAAAGAATATGCATAGAATAATGCATTCTATGTAGCCATGTCACTGTGAATAACGATTTCTTGCATATTTAGCCA
TTTTGATTCCTGTTTGATTTATACTTCTCTGTTGCTACGCAAAACCGATCAAAGAAAAGTGAACTTCAGTTTTACAATCTGTATGCCTAAAAGCGGGTAC
TACCGTTTATTTTACTGACTTGTTTAAATGATTCGCTTTTGTAAGAATCAGATGGCATTATGCTTGTTGTACAATGCCATATTGGTATATGACATAACAG
GAAACAGTATTGTATGATATATTTATAAATGCTATAAAGAAATATTGTGTTTCATGCATTCAGAAATGATTGTTAAAATTCTCCCAACTGGTTCGACCTT
TGCAGATACCCATAACCTATGTTGAGCCTTGCTTACCAGCAAAGAATATTTTTAATGTGGATATCTAATTCTAAAGTCTGTTCCATTAGAAGCAATTGGC
ACATCTTTCTATACTTTATATACTTTTCTCCAGTAATACATGTTTACTTTAAAGATTGTTGCAGTGAAGAAAAACCTTTAACTGAGAAATATGGAAACCG
TCTTAATTTTCCATTGGCTATGATGGAATTAATATTGTATTTTAAAAATGCATATTGATCACTATAATTCTAAAACAATTTTTTAAATAAACCAGCAGGT
TGCTAAAAGAAGGCATTTTATCTAAAGTTATTTTAATAGGTGGTATAGCAGTAATTTTAAATTTAAGAGTTGCTTTTACAGTTAACAATGGAATATGCCT
TCTCTGCTATGTCTGAAAATAGAAGCTATTTATTATGAGCTTCTACAGGTATTTTTAAATAGAGCAAGCATGTTGAATTTAAAATATGAATAACCCCACC
CAACAATTTTCAGTTTATTTTTTGCTTTGGTCGAACTTGGTGTGTGTTCATCACCCATCAGTTATTTGTGAGGGTGTTTATTCTATATGAATATTGTTTC
ATGTTTGTATGGGAAAATTGTAGCTAAACATTTCATTGTCCCCAGTCTGCAAAAGAAGCACAATTCTATTGCTTTGTCTTGCTTATAGTCATTAAATCAT
TACTTTTACATATATTGCTGTTACTTCTGCTTTCTTTAAAAATATAGTAAAGGATGTTTTATGAAGTCACAAGATACATATATTTTTATTTTGACCTAAA
TTTGTACAGTCCCATTGTAAGTGTTGTTTCTAATTATAGATGTAAAATGAAATTTCATTTGTAATTGGAAAAAATCCAATAAAAAGGATATTCATTTAGA
AAATAGCTAAGATCTTTAATAAAAATTTGATATGAAAAGCACAATGTGCAGAAGTTATGGAAAACCTATAGAGGATTACAACAGGTAAACGTTAAAGAGA
ATACATTGCTGACTTATAGTGATGTGGCTAAGAAGTACATGCTTTGTTGTAAAATTGCTTGAAAGCCCATTGAAAGATGTATCTGTTTATTTACAGTCTT
TGAAGTAAAAGTTACCAATGTTTGCCAA

Loop counts:

3 nts: 2
4 nts: 1
5 nts: 3
6 nts: 2
7 nts: 2
8 nts: 1
9 nts: 1

Tetra-loop variants:

GCUA    1

Single bulge variants:

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