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

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

Loop counts:

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

Tetra-loop variants:

GGAA    1
GAAA    1
AGCA    1
UACA    1
CAUG    1
GUCA    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: 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