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

GGGAATCCTGGGATAGTGGCGGACCTGAAGTTGGCCTCTGTGAAGGCTGAGTCCTGGGGAACCGGGACCGAGAAGATTTCGAAGGTGGAGGAGCGTGTCT
CAAGATTGGGGCTACCTGTTCTTTCGTGGGGCAGGGAAGGGGCGGACAGCAGCGCCTATTCTGGAGGAACTGGACTGAGATGTGACCCCGAAGTGTTACC
GCTTCCAAACGAAATGAGGGTCACCTTTCACACCGCCCCCCCCCCGGGGTTGGAAAAGCCACCGATCGTTCCAGCTGCCGAGCAGCTCTTAAAGCTTTGG
ATTCGGCTGTCGTGGAGATAACGGGCACCAGAAAAACTTGTAGGAGTAGCAACAGCTATTTGGTCGGATGGAGGCCAGAAGCCAAGAATAATCGAAACAC
GCTGCCAGCGCCCATTAGATGGATGGGAAATGAGTGTAACTCATTGGGAAAGATATTAGACTTCAAATCACCTAAGGCAAACCCTACTTCCTGGGGCGCG
GGCGCGGGCGCTGGCGTTAGGAGACGTCACTCCCGCGCATAACTGACATGGGGCCCTCTTGGTCGGCGTTTCCGGGCGGGTCCTTCCGACGGCCGCCGCG
GTGATTCCATCACTCGGCTTTCTTCCCGGCCTGCCTCGCGCCCGTAGCCGGGCTGGGCCAGAACAGCCCAAGATGGCCGACTTCGATGATCGTGTGTCGG
ATGAGGAGAAGGTACGCATAGCTGCTAAATTCATCACTCATGCACCCCCAGGGGAATTTAATGAAGTATTCAATGACGTTCGGCTACTACTTAATAATGA
CAATCTCCTCAGGGAAGGGGCAGCACATGCATTTGCCCAGTATAACATGGATCAGTTCACGCCTGTGAAGATAGAAGGATATGAAGATCAGGTCTTAATT
ACAGAGCACGGTGACCTGGGTAATAGCAGATTTTTAGATCCAAGAAACAAAATTTCCTTTAAATTTGACCACTTACGGAAAGAAGCAAGTGACCCCCAGC
CAGAAGAAGCAGATGGAGGTCTGAAGTCTTGGAGAGAATCCTGTGACAGTGCTTTAAGAGCCTATGTGAAAGACCATTATTCCAACGGCTTCTGTACTGT
TTATGCTAAAACTATCGATGGGCAACAGACTATTATTGCATGTATTGAAAGCCACCAGTTTCAGCCTAAAAACTTCTGGAATGGTCGTTGGAGATCAGAG
TGGAAGTTCACCATCACACCACCTACAGCCCAGGTGGTTGGCGTGCTTAAGATTCAGGTTCACTATTATGAAGATGGCAATGTTCAGTTGGTTAGTCATA
AAGATGTACAGGATTCACTAACTGTTTCGAATGAAGCCCAAACTGCCAAGGAGTTTATTAAAATCATAGAGAATGCAGAAAATGAGTATCAGACAGCAAT
TAGTGAAAACTATCAAACAATGTCAGATACCACATTCAAGGCCTTGCGCCGGCAGCTTCCAGTTACCCGCACCAAAATCGACTGGAACAAGATACTCAGC
TACAAGATTGGCAAAGAAATGCAGAATGCTTAAAGGCTGAATGTAGGATTCTTCAGTATGTGGAAAGACAAGGATTCAACGTGTGGTCATATGATAAATA
AGTGATTTATAAACAAGAGTGATATTTTGCTAGGGCTTTCAAAGTTAACCGGTTTTCTAGCCTCATGGAATACTGTTGAACCTATAGCGTTGTCTTGATT
CTTTTGTGTTCTCTGCCTTGTAATTTTCTGTTACTGCTATATCTACGTGTAAATCTTTTTTTCTTTTTTTTTTTTTTTTTTTGGTTAATTCTGCCACATT
TAATGTTGGTGAGAGAGTGATCTATCCTAATGACATTTTACTGTTTAAAAAAGTTTCCTAGCCATGAAGCCCTGCTACTGATTTAGACAAGGTATTATGG
TCATTACTTTGTACCCCTATCCTTCCAAGCACTTCTGGTACTTCAGTCGTTTTTACTGATCCACCAACACCTAAAGAGGCTATGCTACAGTCTCTAGCTA
AATGGAAGACACATTCATCCTTCTCCCTCTGACTGCTTTGATCATCATTTATTGCATCTCATAACTAATTTTCTAAAGTTTGGATTGGGACTTTTCAGGT
CCTTTTTGGAGGGCAAAGGAAGTGCCAGCTTCTCTGGGGAACTTGTTTTTAAATCCAAAGACTTGAACCACATTCCCTGCACATGAACATGTTTGCTTTT
ATCCCTTCTCTCATTGTCTCCTTCCCATCTTAGTACCATTGTAGTTATAAACATCTGCATTTTTTAGAAGCATTTTACCCATTTATTTTTTTAAACATTC
AAGAACTGCTGACGTACTGTGGATGTAGAGTATAAAACTTGAAAAATGCAGATGTTGAAGGAATAATAGGTATCTTGTGCTTTAATACTTTATGGCAGGA
TTGTACTATAAGCAAATGAATTAAACAGCTATGTAAATCATAAAGAAAAACTAAAAATGAACCAAAGTGAAAGGATAACTTCCAGGCAGTATCTTTCTAT
TGTAACCTGTTATTTAAGGAAATACTAGTGATTTCTTCTAAATAGGATGTAAAACTTCTTTCAAATTACTCTTCCTCAGTCCTGCCTGCCAAGAACTCAA
GTGTAACTGTGATAAAATAACCTTTCCCAGGTATATTGGCAGGTATGTGTGTAATCTCAGAATACACAGGTGACATAGATATGATATGACAACTGGTAAT
GGTGGATTCATTTACATTGTTTACACTTCTATGACCAGGCCTTAAGGGAAGGTCAGTTTTTTAAAAAACCAAGTAGTGTCTTCCTACCTATCTCCAGATA
CATGTCAAAAAAAGAAAGGTGTTTGTGCTTCCGTTTTGTTTCTGCTCAGTAATATAGTCAAGCAAGTTTGTTCCAGGTGACCCATTGAGCTGTGTATGCA
TTTTTGTTTATTTCAATAAAATATATTTGTATTATTTGTCCTTCATACTATCCATCCATACCACACTATCTTCTGTATCAGGTAGTCTAATAGAAATATA
CCTGTTTTGTTCTAAAATTG

Loop counts:

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

Tetra-loop variants:

AGUU    1
GAAA    1
UUCU    1

Single bulge variants:

G x 0 bulge: 2
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: 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: 0
C x G bulge: 0
C x A bulge: 1
C x U bulge: 0
C x C bulge: 0