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

GAGCCGCTCCTGACCCACCTACCCCAGCTCTCGCGCCGCGTGCAGAGGTGCTCAAGCCTCCTCGCGGTCCGCAGTCAGTGCCGCCGCGCCCGGCCTCCCG
CACGCCCCGCAGGTAGCGCCCCCGCCCGCGGCCCAGAGTGCGCTCGCGCCGGCACCAGCTCCCGGATAAACGGCGCGCCGCGCGGAGATGACAGCCGAGG
AGATGAAGGCGACCGAGAGCGGGGCGCAGTCGGCGCCGCTGCCCATGGAGGGAGTGGACATCAGCCCCAAACAGGACGAAGGCGTGCTGAAGGTCATCAA
GAGAGAGGGCACAGGTACAGAGATGCCCATGATTGGGGACCGAGTCTTTGTCCACTACACTGGCTGGCTATTAGATGGCACAAAGTTTGACTCCAGTCTG
GATCGCAAGGACAAATTCTCCTTTGACCTGGGAAAAGGGGAGGTCATCAAGGCTTGGGACATTGCCATAGCCACCATGAAGGTGGGGGAGGTGTGCCACA
TCACCTGCAAACCAGAATATGCCTACGGTTCAGCAGGCAGTCCTCCAAAGATTCCCCCCAATGCCACGCTTGTATTTGAGGTGGAGTTGTTTGAGTTTAA
GGGAGAAGATCTGACGGAAGAGGAAGATGGCGGAATCATTCGCAGAATACAGACTCGCGGTGAAGGCTATGCTAAGCCCAATGAGGGTGCTATCGTGGAG
GTTGCACTGGAAGGGTACTACAAGGACAAGCTCTTTGACCAGCGGGAGCTCCGCTTTGAGATTGGCGAGGGGGAGAACCTGGATCTGCCTTATGGTCTGG
AGAGGGCCATTCAGCGCATGGAGAAAGGAGAACATTCCATCGTGTACCTCAAGCCCAGCTATGCTTTTGGCAGTGTTGGGAAGGAAAAGTTCCAAATCCC
ACCAAATGCTGAGCTGAAATATGAATTACACCTCAAGAGTTTTGAAAAGGCCAAGGAGTCTTGGGAGATGAATTCAGAAGAGAAGCTGGAACAGAGCACC
ATAGTGAAAGAGCGGGGCACTGTGTACTTCAAGGAAGGTAAATACAAGCAAGCTTTACTACAGTATAAGAAGATCGTGTCTTGGCTGGAATATGAGTCTA
GTTTTTCCAATGAGGAAGCACAGAAAGCACAGGCCCTTCGACTGGCCTCTCACCTCAACCTGGCCATGTGTCATCTGAAACTACAGGCCTTCTCTGCTGC
CATTGAAAGCTGTAACAAGGCCCTAGAACTGGACAGCAACAACGAGAAGGGCCTCTTCCGCCGGGGAGAGGCCCACCTGGCCGTGAATGACTTTGAACTG
GCACGGGCTGATTTCCAGAAGGTCCTGCAGCTCTACCCCAACAACAAAGCCGCCAAGACCCAGCTGGCTGTGTGCCAGCAGCGGATCCGAAGGCAGCTTG
CCCGGGAGAAGAAGCTCTATGCCAATATGTTTGAGAGGCTGGCTGAGGAGGAGAACAAGGCCAAGGCAGAGGCTTCCTCAGGAGACCATCCCACTGACAC
AGAGATGAAGGAGGAGCAGAAGAGCAACACGGCAGGGAGCCAGTCTCAGGTGGAGACAGAAGCATAGCCCCTCTCCACCAGCCCTACTCCTGCGGCTGCC
TGCCCCCCAGTCTCCCCACTCCACCCTGTTAGTTTTGTAAAAACTGAAGAATTTTGAGTGAATTAGACCTTTATTTTTCTATCTGGTTGGATGGTGGCTT
TAGGGGAAGGGGGAAAGGTGTAGGCTGGGGGATTGAGGTGGGGAATCATTTTAGCTGGTGTCAGCCCCTCTTCCCTTCCTCCATTGCACATGAACATATG
TCCATCCATATATATTCATCAGAATGTTAATTTATTTTGCTCCCTCTGTTAGGTCCATTTTCTAAGGGTAGAAGAGGCAAGTGGTAGGGATGAGGTCTGA
TAAGAACCCAGGGTGGAGAGGGAGACTCCTGGGCAGCCGTTTTCCTCATCCTTTCCCTCTCCCAGTCCATTTCCAAATGTGGCCTCCATGTGGGTGCTAG
GGACATGGGAAAAACCACTGCTATGCCATTTCTTCTCTCTGTTCCCTTCCTCACCCCCGACGGTGTGGCTGATGATGTCTTCTGGTGTCATGGTGACCAC
CCCCTGTTCCCTGTTCTGGTATTTCCCCTGTCAGTTTCCCCTCTCGGCCAGGTTGTGTCCCAAAATCCCCTCAGCCTCTTCTCTGCACGTTGCTGAAGGT
CCAGGCTTGCCTCAAGTTCCATGCTTGAGCAATAAAGTGGAAACAATAAAACCTGGGTGTCAGACAACCCTTTCTGTTCAGCCTTGGAGTGGTGGGTATG
GGTGGGTACATAATGGGTAGTAGCACAATCAAGGGGTCACCCACTTAGTTCCAGTTGAGCTTAAATAAGTGAGCATCTCATGTAGATGCCATAGTTGGGC
AGGAAGCAGCCCCACCATGCATGGCTTCCTGAGCACTGCACAGGCTGCCGCTGGGATTTGTGTCTATGGCTTCGCCCAAGGTTCCCAGCACTCCCTCCCT
CCAGCAACCTGGCAGTTTTAGTGCCTCTGGTTTTCTTCCCTGACACTTAGGAAGACGAAAGTATAAAGATCTAGAAGACTGGGACACCATGCATGTTCAT
TTTGAAGTTGGAATTGGTCTTCTGCCTACCTCTGATCTGGCAGAGGTATCTGCATTTTGGTTTGTTAACAAGGTAAAACTCCTGGTGTCACTGACCTCCT
CCTGTCAGATAACTTACATGATTAAGGTTAAGAGTAAAGCAGAGTGTTCACGTCCAGCTTCCTTCTCAGCCTTAACAGGAAAAGGCTTGTGCTTTTTTTC
TAACTATGCTTTGACCCTTAACTCCTATGGCATGATGGGGCCCTGGGAGAAGCCAGGCAGCACAAGCCAGTCATGCTGAGCTGCCTCCAGATAATCCTGG
CTCCAGGCCAGAGCCCGTGTCTGCCCTCATCCCTCTCTCCTACTGTGAGCTCTCCAGTCCTTTCCCAACAGCGATGTGGTTGTCTGCTTAGCCACATGCC
TGTATAGTTCCTTCCAGAAGAAATGTATAATGGTGGAAGATGTATTTCTGTGTGAAAATTTTCACCAAGTCATACAACACAGCTGATGCTGGAGCCAGGA
TTAAAATTGGGGTGTACAAGTCTCCCAGTGTGAGTATCCCTTGAGCCCAAGACACCAAGGATGCAGAGAACTGTGACTGTGCCACTGCACGCCAGCCTGG
GCAAGAGAGTGAGACCATCTCTTTTTTAAAAAAGTCCCTGTGTAACTGCTTTCTTACTGGGCTTACCTCACATCACAGCCCTGTGTTTGTGGTTTGTGTC
TGGGTCCTCTTGGTATTTCAAAAGTAGTAGATTCTTACGCCTGCAGCCAACAATAATCACTAACTCAAGCATTTATGGAGTAAGCCTAGCACTGTACTGA
CAGCATCACATGAGTGAAACTGAATCCTTGCAACCATCCTACAAAGAAGGTATAACTTTAATAACCCTATTTACAGATAAGAAAACCAAGACTCAGAAGT
TAAATGGAAAGGTGAGGTCTCTGAACTAATCCAGACTCTCCCATGAGGTTCCTTTGGCAAGTCCTGGGCTTCTGTCCTCATCTGCAAAATCGAAAGCATT
CCTGAGGTTTCTTCCAGCTCTGCATCCTGTAGGATTCCAAGAATGTAAAACTGCATGTAACCGTGGAACATCTAGAGATAAGTCTTAGTTTATGTAACAT
TAAAACTGTCTAGTGAGGATGTTTTGTTAAAA

Loop counts:

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

Tetra-loop variants:

GCCG    1
GUGU    1
UUCU    1
AUCA    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: 0
U x C bulge: 1
C x G bulge: 0
C x A bulge: 1
C x U bulge: 1
C x C bulge: 0