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

GTAGGAAGGGGCGGGGCTTTGCCGAAGGGGGCGGGGCTCTCGCTGATGGGTTGGCTTTCGTCAGGGACATAGGTAGAAGCTGGTTGGGGAGTGTGCGTGC
CAGCCTGACGCGATATAGTGCGCACATGCGTGATGACGTAGAGGGCGTTGATTGGGACCGAGTACAGGGCCCGCGCATGCGTGGATTGTCGTCTTCTGTC
CAAGTTGGTCGCTTCCCTGCGCCAAAGTGAGCAGTAGCCAACATGTCAGGGTGGGAGTCATATTACAAAACCGAGGGCGATGAAGAAGCAGAGGAAGAAC
AAGAAGAGAACCTTGAAGCAAGTGGAGACTATAAATATTCAGGAAGAGATAGTTTGATTTTTTTGGTTGATGCCTCCAAGGCTATGTTTGAATCTCAGAG
TGAAGATGAGTTGACACCTTTTGACATGAGCATCCAGTGTATCCAAAGTGTGTACATCAGTAAGATCATAAGCAGTGATCGAGATCTCTTGGCTGTGGTG
TTCTATGGTACCGAGAAAGACAAAAATTCAGTGAATTTTAAAAATATTTACGTCTTACAGGAGCTGGATAATCCAGGTGCAAAACGAATTCTAGAGCTTG
ACCAGTTTAAGGGGCAGCAGGGACAAAAACGTTTCCAAGACATGATGGGCCACGGATCTGACTACTCACTCAGTGAAGTGCTGTGGGTCTGTGCCAACCT
CTTTAGTGATGTCCAATTCAAGATGAGTCATAAGAGGATCATGCTGTTCACCAATGAAGACAACCCCCATGGCAATGACAGTGCCAAAGCCAGCCGGGCC
AGGACCAAAGCCGGTGATCTCCGAGATACAGGCATCTTCCTTGACTTGATGCACCTGAAGAAACCTGGGGGCTTTGACATATCCTTGTTCTACAGAGATA
TCATCAGCATAGCAGAGGATGAGGACCTCAGGGTTCACTTTGAGGAATCCAGCAAGCTAGAAGACCTGTTGCGGAAGGTTCGCGCCAAGGAGACCAGGAA
GCGAGCACTCAGCAGGTTAAAGCTGAAGCTCAACAAAGATATAGTGATCTCTGTGGGCATTTATAATCTGGTCCAGAAGGCTCTCAAGCCTCCTCCAATA
AAGCTCTATCGGGAAACAAATGAACCAGTGAAAACCAAGACCCGGACCTTTAATACAAGTACAGGCGGTTTGCTTCTGCCTAGCGATACCAAGAGGTCTC
AGATCTATGGGAGTCGTCAGATTATACTGGAGAAAGAGGAAACAGAAGAGCTAAAACGGTTTGATGATCCAGGTTTGATGCTCATGGGTTTCAAGCCGTT
GGTACTGCTGAAGAAACACCATTACCTGAGGCCCTCCCTGTTCGTGTACCCAGAGGAGTCGCTGGTGATTGGGAGCTCAACCCTGTTCAGTGCTCTGCTC
ATCAAGTGTCTGGAGAAGGAGGTTGCAGCATTGTGCAGATACACACCCCGCAGGAACATCCCTCCTTATTTTGTGGCTTTGGTGCCACAGGAAGAAGAGT
TGGATGACCAGAAAATTCAGGTGACTCCTCCAGGCTTCCAGCTGGTCTTTTTACCCTTTGCTGATGATAAAAGGAAGATGCCCTTTACTGAAAAAATCAT
GGCAACTCCAGAGCAGGTGGGCAAGATGAAGGCTATCGTTGAGAAGCTTCGCTTCACATACAGAAGTGACAGCTTTGAGAACCCCGTGCTGCAGCAGCAC
TTCAGGAACCTGGAGGCCTTGGCCTTGGATTTGATGGAGCCGGAACAAGCAGTGGACCTGACATTGCCCAAGGTTGAAGCAATGAATAAAAGACTGGGCT
CCTTGGTGGATGAGTTTAAGGAGCTTGTTTACCCACCAGATTACAATCCTGAAGGGAAAGTTACCAAGAGAAAACACGATAATGAAGGTTCTGGAAGCAA
AAGGCCCAAGGTGGAGTATTCAGAAGAGGAGCTGAAGACCCACATCAGCAAGGGTACGCTGGGCAAGTTCACTGTGCCCATGCTGAAAGAGGCCTGCCGG
GCTTACGGGCTGAAGAGTGGGCTGAAGAAGCAGGAGCTGCTGGAAGCCCTCACCAAGCACTTCCAGGACTGACCAGAGGCCGCGCGTCCAGCTGCCCTTC
CGCAGTGTGGCCAGGCTGCCTGGCCTTGTCCTCAGCCAGTTAAAATGTGTTTCTCCTGAGCTAGGAAGAGTCTACCCGACATAAGTCGAGGGACTTTATG
TTTTTGAGGCTTTCTGTTGCCATGGTGATGGTGTAGCCCTCCCACTTTGCTGTTCCTTACTTTACTGCCTGAATAAAGAGCCCTAAGTTTGTACTA

Loop counts:

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

Tetra-loop variants:

AGGU    1
CAAG    1
UGUU    1
UUCA    1

Single bulge variants:

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