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

CGCGGTCCTCGGAGACACGCGGCGGTGTCCTGTGTTGGCCATGGCCGACTACCTGATTAGTGGGGGCACGTCCTACGTGCCAGACGACGGACTCACAGCA
CAGCAGCTCTTCAACTGCGGAGACGGCCTCACCTACAATGACTTTCTCATTCTCCCTGGGTACATCGACTTCACTGCAGACCAGGTGGACCTGACTTCTG
CTCTGACCAAGAAAATCACTCTTAAGACCCCACTGGTTTCCTCTCCCATGGACACAGTCACAGAGGCTGGGATGGCCATAGCAATGGCGCTTACAGGCGG
TATTGGCTTCATCCACCACAACTGTACACCTGAATTCCAGGCCAATGAAGTTCGGAAAGTGAAGAAATATGAACAGGGATTCATCACAGACCCTGTGGTC
CTCAGCCCCAAGGATCGCGTGCGGGATGTTTTTGAGGCCAAGGCCCGGCATGGTTTCTGCGGTATCCCAATCACAGACACAGGCCGGATGGGGAGCCGCT
TGGTGGGCATCATCTCCTCCAGGGACATTGATTTTCTCAAAGAGGAGGAACATGACTGTTTCTTGGAAGAGATAATGACAAAGAGGGAAGACTTGGTGGT
AGCCCCTGCAGGCATCACACTGAAGGAGGCAAATGAAATTCTGCAGCGCAGCAAGAAGGGAAAGTTGCCCATTGTAAATGAAGATGATGAGCTTGTGGCC
ATCATTGCCCGGACAGACCTGAAGAAGAATCGGGACTACCCACTAGCCTCCAAAGATGCCAAGAAACAGCTGCTGTGTGGGGCAGCCATTGGCACTCATG
AGGATGACAAGTATAGGCTGGACTTGCTCGCCCAGGCTGGTGTGGATGTAGTGGTTTTGGACTCTTCCCAGGGAAATTCCATCTTCCAGATCAATATGAT
CAAGTACATCAAAGACAAATACCCTAATCTCCAAGTCATTGGAGGCAATGTGGTCACTGCTGCCCAGGCCAAGAACCTCATTGATGCAGGTGTGGATGCC
CTGCGGGTGGGCATGGGAAGTGGCTCCATCTGCATTACGCAGGAAGTGCTGGCCTGTGGGCGGCCCCAAGCAACAGCAGTGTACAAGGTGTCAGAGTATG
CACGGCGCTTTGGTGTTCCGGTCATTGCTGATGGAGGAATCCAAAATGTGGGTCATATTGCGAAAGCCTTGGCCCTTGGGGCCTCCACAGTCATGATGGG
CTCTCTCCTGGCTGCCACCACTGAGGCCCCTGGTGAATACTTCTTTTCCGATGGGATCCGGCTAAAGAAATATCGCGGTATGGGTTCTCTCGATGCCATG
GACAAGCACCTCAGCAGCCAGAACAGATATTTCAGTGAAGCTGACAAAATCAAAGTGGCCCAGGGAGTGTCTGGTGCTGTGCAGGACAAAGGGTCAATCC
ACAAATTTGTCCCTTACCTGATTGCTGGCATCCAACACTCATGCCAGGACATTGGTGCCAAGAGCTTGACCCAAGTCCGAGCCATGATGTACTCTGGGGA
GCTTAAGTTTGAGAAGAGAACGTCCTCAGCCCAGGTGGAAGGTGGCGTCCATAGCCTCCATTCGTATGAGAAGCGGCTTTTCTGAAAAGGGATCCAGCAC
ACCTCCTCGGTTTTTTTTTCAATAAAAGTTTAGAAAGAAAAAA

Loop counts:

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

Tetra-loop variants:

GAAA    1
GAGC    1
AGCA    1
CAUG    1
GUCA    1

Single bulge variants:

G x 0 bulge: 0
A x 0 bulge: 5
U x 0 bulge: 5
C x 0 bulge: 4

1 x 1 internal loop variants:

G x G bulge: 0
G x A bulge: 2
G x U bulge: 0
G x C bulge: 0
A x G bulge: 2
A x A bulge: 0
A x U bulge: 0
A x C bulge: 3
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: 3
C x U bulge: 0
C x C bulge: 0