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

GTACATGACCGGCATCGACTAATCAGGGCCAGGCTCGATGAGGCTTTGTCTCCCTACCGCGCGCGGGGCCGATTCTCCCGCCTCCCAGCCCCGGCGCACG
CGCGCCCCGCCCAGCCTGCTTTCCCTCCGCGCCCTCCCCTCTCCTTTCTCCCTCTCAGAACCTTCCTGCCGTCGCGTTTGCACCTCGCTGCTCCAGCCTC
TGGGGCGCATTCCAACCTTCCAGCCTGCGACCTGCGGAGAAAAAAAATTACTTATTTTCTTGCCCCATACATACCTTGAGGCGAGCAAAAAAATTAAATT
TTAACCATGAGGGAAATCGTGCACATCCAGGCTGGTCAGTGTGGCAACCAGATCGGTGCCAAGTTCTGGGAGGTGATCAGTGATGAACATGGCATCGACC
CCACCGGCACCTACCACGGGGACAGCGACCTGCAGCTGGACCGCATCTCTGTGTACTACAATGAAGCCACAGGTGGCAAATATGTTCCTCGTGCCATCCT
GGTGGATCTAGAACCTGGGACCATGGACTCTGTTCGCTCAGGTCCTTTTGGCCAGATCTTTAGACCAGACAACTTTGTATTTGGTCAGTCTGGGGCAGGT
AACAACTGGGCCAAAGGCCACTACACAGAGGGCGCCGAGCTGGTTGATTCTGTCCTGGATGTGGTACGGAAGGAGGCAGAGAGCTGTGACTGCCTGCAGG
GCTTCCAGCTGACCCACTCACTGGGCGGGGGCACAGGCTCTGGAATGGGCACTCTCCTTATCAGCAAGATCCGAGAAGAATACCCTGATCGCATCATGAA
TACCTTCAGTGTGGTGCCTTCACCCAAAGTGTCTGACACCGTGGTCGAGCCCTACAATGCCACCCTCTCCGTCCATCAGTTGGTAGAGAATACTGATGAG
ACCTATTGCATTGACAACGAGGCCCTCTATGATATCTGCTTCCGCACTCTGAAGCTGACCACACCAACCTACGGGGATCTGAACCACCTTGTCTCAGCCA
CCATGAGTGGTGTCACCACCTGCCTCCGTTTCCCTGGCCAGCTCAATGCTGACCTCCGCAAGTTGGCAGTCAACATGGTCCCCTTCCCACGTCTCCATTT
CTTTATGCCTGGCTTTGCCCCTCTCACCAGCCGTGGAAGCCAGCAGTATCGAGCTCTCACAGTGCCGGAACTCACCCAGCAGGTCTTCGATGCCAAGAAC
ATGATGGCTGCCTGTGACCCCCGCCACGGCCGATACCTCACCGTGGCTGCTGTCTTCCGTGGTCGGATGTCCATGAAGGAGGTCGATGAGCAGATGCTTA
ACGTGCAGAACAAGAACAGCAGCTACTTTGTGGAATGGATCCCCAACAATGTCAAGACAGCCGTCTGTGACATCCCACCTCGTGGCCTCAAGATGGCAGT
CACCTTCATTGGCAATAGCACAGCCATCCAGGAGCTCTTCAAGCGCATCTCGGAGCAGTTCACTGCCATGTTCCGCCGGAAGGCCTTCCTCCACTGGTAC
ACAGGCGAGGGCATGGACGAGATGGAGTTCACCGAGGCTGAGAGCAACATGAACGACCTCGTCTCTGAGTATCAGCAGTACCAGGATGCCACCGCAGAAG
AGGAGGAGGATTTCGGTGAGGAGGCCGAAGAGGAGGCCTAAGGCAGAGCCCCCATCACCTCAGGCTTCTCAGTTCCCTTAGCCGTCTTACTCAACTGCCC
CTTTCCTCTCCCTCAGAATTTGTGTTTGCTGCCTCTATCTTGTTTTTTGTTTTTTCTTCTGGGGGGGGTCTAGAACAGTGCCTGGCACATAGTAGGCGCT
CAATAAATACTTGTTTGTTGAATGTCTCCTCTCTCTTTCCACTCTGGGAAACCTAGGTTTCTGCCATTCTGGGTGACCCTGTATTTCTTTCTGGTGCCCA
TTCCATTTGTCCAGTTAATACTTCCTCTTAAAAATCTCCAAGAAGCTGGGTCTCCAGATCCCATTTAGAACCAACCAGGTGCTGAAAACACATGTAGATA
ATGGCCATCATCCTAAGCCCAAAGTAGAAAATGGTAGAAGGTAGTGGGTAGAAGTCACTATATAAGGAAGGGGATGGGATTTTCCATTCTAAAAGTTTTG
GAGAGGGAAATCCAGGCTATTAAAGTCACTAAATTTCTAAGTATGTCCATTTCCCATCTCAGCTTCAAGGGAGGTGTCAGCAGTATTATCTCCACTTTCA
ATCTCCCTCCAAGCTCTACTCTGGAGGAGTCTGTCCCACTCTGTCAAGTGGAATCCTTCCCTTTCCAACTCTACCTCCCTCACTCAGCTCCTTTCCCCTG
ATCAGAGAAAGGGATCAAGGGGGTTGGGAGGGGGGAAAGAGACCAGCCTTGGTCCCTAAGCCTCCAGAAACGTCTTCTTAATCCCCACCTTTTCTTACTC
CCAAAAAAGAATGAACACCCCTGACTCTGGAGTGGTGTATACTGCCACATCAGTGTTTGAGTCAGTCCCCAGAGGAGAGGGGAACCCTCCTCCATCTTTT
TTGCAACATCTCATTTCTTCCTTTTGCTGTTGCTTCCCCCCTCACACACTTGGTTTTGTTCTATCCTACATTTGAGATTTCTATTTTATGTTGAACTTGC
TGCTTTTTTTCATATTGAAAAGATGACATCGCCCCAAGAGCCAAAAATAAATGGGAATTGAAAAAAGCTG

Loop counts:

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

Tetra-loop variants:

AGAU    1
GCCU    1
UUCU    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: 1
A x U bulge: 0
A x C bulge: 1
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: 1
C x U bulge: 0
C x C bulge: 0