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

GGACTTCCGGCGGGTGACGCGCCCGGGTTCGGCTACAAAAGAGGACGGCTGCGGCGCGCCGGGCGGAACTTTCCAGAACGCTCGGTGAGAGGCGGAGGAG
CGGTAACTACCCCGGCTGCGCACAGCTCGGCGCTCCTTCCCGCTCCCTCACACACCGGCCTCAGCCCGCACCGGCAGTAGAAGATGGTGAAAGAAACAAC
TTACTACGATGTTTTGGGGGTCAAACCCAATGCTACTCAGGAAGAATTGAAAAAGGCTTATAGGAAACTGGCTTTGAAGTACCATCCTGATAAGAACCCA
AATGAAGGAGAGAAGTTTAAACAGATTTCTCAAGCTTACGAAGTTCTCTCTGATGCAAAGAAAAGGGAATTATATGACAAAGGAGGAGAACAGGCAATTA
AAGAGGGTGGAGCAGGTGGCGGTTTTGGCTCCCCCATGGACATCTTTGATATGTTTTTTGGAGGAGGAGGAAGGATGCAGAGAGAAAGGAGAGGTAAAAA
TGTTGTACATCAGCTCTCAGTAACCCTAGAAGACTTATATAATGGTGCAACAAGAAAACTGGCTCTGCAAAAGAATGTGATTTGTGACAAATGTGAAGGT
AGAGGAGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAATTGCCGAGGTACTGGAATGCAAATAAGAATTCATCAGATAGGACCTGGAATGGTTCAGCAAA
TTCAGTCTGTGTGCATGGAGTGCCAGGGCCATGGGGAGCGGATCAGTCCTAAAGATAGATGTAAAAGCTGCAACGGAAGGAAGATAGTTCGAGAGAAGAA
AATTTTAGAAGTTCATATTGACAAAGGCATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAGGAGACCAAGAACCAGGACTGGAGCCAGGCGATATT
ATCATTGTGTTAGATCAGAAGGACCATGCTGTTTTTACTCGACGAGGAGAAGACCTTTTCATGTGTATGGACATACAGCTCGTTGAAGCACTGTGTGGCT
TCCAGAAGCCAATATCTACTCTTGACAACCGAACCATCGTCATCACCTCTCATCCAGGTCAGATTGTCAAGCATGGAGATATCAAGTGTGTACTAAATGA
AGGCATGCCAATTTATCGTAGACCATATGAAAAGGGTCGCCTAATCATCGAATTTAAGGTAAACTTTCCTGAGAATGGCTTTCTCTCTCCTGATAAACTG
TCTTTGCTGGAAAAACTCCTACCCGAGAGGAAGGAAGTGGAAGAGACTGATGAGATGGACCAAGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGAC
GGCGCCACTACAATGGAGAAGCATATGAGGATGATGAACATCATCCCAGAGGTGGTGTTCAGTGTCAGACCTCTTAATGGGCCAGTGAATAACACTCACT
GCTGGCATTTAATGTGCAGTAGTGAATGAGTGAAGGACTGTAATCATAATATGCTCACTACTTGCTCTTGTTTTTGTTTTAATAAACTATAGTAGTGTTT
TAAAAAGTTAAATGAAGAATAAACGCAAATATAAAAGCTCTGATTTTGCCCTGTATGTATGATGACTTCAGTGTGCAAGATGAAGTTTAATACCTGTAAA
AACTACAAAGAAGTTCCCCTAGCATTTCTAGGCCAAACCTTGTAATTGACTTCAGCTATGTACGTGGACAAGCTTAGACTGAAATGCTAGGTATATGTAT
TGGCTTCAGTGTATGACCCTTCATTGTTAAGCTATGAAAGTAAAACTCTGTATTTAACTGGCAATGAGGAAAAAAAAATTTTGTAGAGAAGTGTTGGTCT
GTATAGTTCTTTATATTAAGTGGGATTCATTGTAATGCCTCTGCATTTATTCTGTTGCCTCAGCTGTTACTTGAAGATGGCGTAATATATAATTTATCCT
GTGGTATCAGTGATAAAAATGATACCTTTCTGTAGGAGGGGTTTATCATAATATGCTGCTTCTTGAAGGCTTGCACTTCCAGAATTGTGTTTCCTTCTGC
TGTGCCATTCATATATATATACATATATATATATAATCTTGACCAGTCCTGGTCATTTGCTCCCCTCCTTGTCTGTGGACCATGATAAGCCCAAGTAGTG
ACTTCAGAGCTGGGTAACAGAAATTAAAGTGAAAAGACCTTTACGTGGAGAATTTGCATGCGTAATATAGGAAGGTGTTCTTTAGGTATGTTACAGGATT
ACTTTAAACCATTTGACTTTCGCTCCAAAGTTATGTTGGTAGTATAGCAAATTATGATGAATAGCTTTAATTGTATGTTTAAAAGTCTCATATGTTCACA
TGCTTAAATCTGGGTATCAGAATTTAAGCAATTCTTGAAATGTATTGTCTCCTTAATATACTAATTACAAAGCATCTCCAA

Loop counts:

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

Tetra-loop variants:

ACCA    1
GUCC    1
GAAA    1
AAAC    1
CGCA    1
CCAG    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 2
U x 0 bulge: 2
C x 0 bulge: 0

1 x 1 internal loop variants:

G x G bulge: 1
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