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

CTTCCGCTCCCGGAGCGCGTGCGCCCTCTTACTCGGCTCCCCTTGGTTTCCTGGGGTCCTGCCCCTTCAAGCTGGGGCGGGAGCGGAGGACCCCGCTCTC
AGGGGTTGCCGGACCATGCGTTGGGGGCTGCGCCCTCGCGGGCCGGGCGCGGCCGCCCTGGCCACTGCCCGAAGTTTGTGGGGGACGCCCCGCCTTCCCT
GCAGCCCGGGATGGCAAGGGGCGACGAAGAGGCTTCTGGTGCGGTCGGTCTCCGGGGCCAGTAACCACCAGCCGAACTCGAATAGTGGCAGATACCGGGA
CACGGTGCTGCTGCCGCAGACGAGCTTCCCCATGAAGCTGCTGGGCCGCCAGCAGCCGGACACGGAGCTGGAGATCCAGCAGAAATGTGGATTTTCAGAA
CTTTATTCATGGCAAAGAGAAAGAAAAGTAAAGACAGAATTTTGCCTTCATGATGGACCTCCTTATGCAAACGGTGACCCTCATGTTGGACATGCTTTAA
ATAAGATTTTGAAAGACATAGCCAATCGATTCCATATGATGAATGGCTCCAAAATACATTTTGTGCCCGGCTGGGATTGTCATGGGTTGCCCATTGAAAT
AAAAGTATTATCAGAACTTGGTAGAGAAGCTCAGAATCTTTCAGCTATGGAAATTAGAAAGAAAGCTAGATCATTTGCTAAAGCAGCCATTGAGAAACAG
AAATCAGCATTTATTCGTTGGGGAATAATGGCAGATTGGAATAATTGCTACTATACATTTGATGGGAAGTATGAAGCCAAACAGTTGAGAACTTTTTACC
AAATGTATGATAAGGGCTTGGTTTATCGATCTTACAAACCTGTGTTTTGGTCTCCGTCATCTAGGACTGCATTGGCTGAAGCAGAACTTGAATATAATCC
TGAGCATGTCAGTCGTTCAATATATGTAAAATTTCCTCTCTTAAAGCCTTCTCCAAAATTGGCATCTCTTATAGATGGTTCATCTCCTGTTAGTATTTTG
GTCTGGACCACACAACCTTGGACGATTCCAGCCAATGAAGCTGTTTGCTATATGCCTGAATCAAAGTATGCTGTTGTGAAATGTTCTAAGTCTGGAGACC
TCTACGTACTGGCGGCAGATAAAGTAGCATCTGTTGCTTCTACTTTGGAAACAACATTTGAGACTATTTCAACACTTTCAGGTGTAGATTTGGAAAATGG
TACTTGCAGTCATCCATTAATTCCTGATAAAGCCTCTCCTCTTTTACCTGCAAATCATGTGACCATGGCAAAAGGAACGGGATTGGTTCACACAGCCCCA
GCTCATGGTATGGAAGACTACGGTGTAGCGTCTCAGCACAACCTGCCCATGGATTGTCTAGTGGACGAAGATGGAGTTTTCACAGATGTTGCAGGTCCTG
AACTTCAAAACAAGGCTGTCCTTGAAGAGGGAACTGATGTGGTTATAAAGATGCTTCAGACTGCAAAGAATTTGTTGAAAGAGGAGAAATTGGTGCATAG
CTATCCGTATGACTGGAGGACCAAGAAACCTGTGGTTATTCGTGCCAGCAAGCAGTGGTTTATAAACATCACGGATATTAAGACTGCAGCCAAGGAATTG
TTAAAAAAGGTGAAATTTATTCCTGGATCAGCACTGAATGGCATGGTTGAAATGATGGACAGGCGGCCATATTGGTGTATATCAAGGCAAAGAGTTTGGG
GTGTTCCAATTCCTGTGTTTCATCATAAGACCAAGGATGAATACTTGATCAACAGCCAAACCACTGAGCATATTGTTAAACTAGTGGAACAACACGGCAG
TGATATCTGGTGGACTCTTCCCCCTGAACAACTTCTTCCAAAAGAAGTCTTATCTGAGGTTGGTGGCCCTGATGCCTTGGAATATGTGCCAGGTCAGGAT
ATTTTGGACATCTGGTTTGATAGCGGAACTTCATGGTCTTATGTTCTTCCAGGTCCTGACCAAAGAGCAGATTTGTACTTGGAAGGAAAAGACCAGCTCG
GGGGTTGGTTTCAGTCATCCTTATTAACAAGTGTGGCAGCAAGGAAGAGAGCACCTTATAAGACAGTGATTGTTCATGGATTTACCCTTGGAGAAAAGGG
AGAAAAGATGTCCAAGTCTCTTGGGAATGTCATTCATCCTGATGTTGTCGTTAATGGAGGACAAGATCAAAGCAAAGAGCCTCCGTATGGTGCTGATGTC
CTTCGCTGGTGGGTAGCTGATTCCAATGTCTTCACCGAAGTTGCAATTGGCCCATCCGTGCTCAATGCTGCCAGAGATGATATTAGCAAGCTTAGGAATA
CACTTCGCTTTCTTTTGGGAAATGTGGCTGATTTCAACCCAGAAACAGATTCCATCCCTGTAAACGATATGTATGTCATAGACCAGTACATGCTACACTT
ACTGCAGGATTTGGCAAACAAGATTACCGAATTATACAAACAATATGATTTTGGAAAAGTTGTTCGGCTGTTACGGACGTTTTATACCAGAGAGCTCTCT
AACTTTTATTTCAGTATAATCAAAGATAGGCTCTATTGTGAAAAGGAAAATGACCCCAAACGACGCTCTTGTCAGACTGCATTAGTTGAAATTTTGGATG
TAATAGTTCGTTCTTTTGCTCCCATTCTTCCTCACCTGGCTGAAGAGGTGTTCCAGCACATACCTTATATTAAAGAGCCCAAGAGTGTTTTCCGTACTGG
GTGGATTAGTACTAGTTCTATCTGGAAAAAGCCCGGGTTGGAAGAAGCTGTGGAGAGTGCGTGTGCAATGCGAGACTCATTTCTTGGAAGCATCCCTGGC
AAAAATGCAGCTGAGTACAAGGTTATCACTGTGATAGAACCTGGACTGCTTTTTGAGATAATAGAGATGCTGCAGTCTGAAGAGACTTCCAGCACCTCTC
AGTTGAATGAATTAATGATGGCTTCTGAGTCAACTTTACTGGCTCAGGAACCACGAGAGATGACTGCAGATGTAATCGAGCTTAAAGGGAAATTCCTCAT
CAACTTAGAAGGTGGTGATATTCGTGAAGAGTCTTCCTATAAAGTAATTGTCATGCCGACTACGAAAGAAAAATGCCCCCGTTGTTGGAAGTATACAGCG
GAGTCTTCAGATACACTGTGTCCTCGATGTGCAGAAGTTGTCAGTGGAAAATAGTATTAACAGCTCACTCGAGCAAGAACCCTCCTGACAGTACTGGCTA
GAAGTTTGGATGGATTATTTACAATATAGGAAAGAAAGCCAAGATTTAGGTAATGAGTGGATGAGTAAATGGTGGAGGATGGGAGTCAAAATCAGAATTA
TAGAAGAAGTATTTCCTGTAACTATAGAAAGAATTATGTATATATACATGCAGAAATATATATGTGTGTGTGTATCTGTGGATGGATATATGTATATCTC
TTCCTATATATATCCATAGTGGACTTATTCAGAACATAGATATGTATTCAGCTTGTCTTCAAATACGGCCAAGCAGAAAATGTTTTATATTTTATAAATC
ATCTTTTGACTCTGTATTTAAATTCTATGATACTGAAAATAAAGGCATTCTGGAAAAATA

Loop counts:

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

Tetra-loop variants:

GAAG    2
CCAA    1
AUAU    1
AAUG    1
ACUC    1
GCCG    1
AACU    1
AAAG    1

Single bulge variants:

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

1 x 1 internal loop variants:

G x G bulge: 2
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